
#######################################################
#                                                     #
#                        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   63 (  539),  selected   63 , name one
# Molecule2: number of CA atoms  105 (  864),  selected   63 , 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:    38      24_A - 61_A        4.56    15.41
  LCS_AVERAGE:     32.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34      24_A - 57_A        1.78    18.46
  LCS_AVERAGE:     24.58

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      24_A - 40_A        0.79    16.28
  LCS_AVERAGE:     12.17

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     V    24_A     V    24_A     17   34   38      4   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     H    25_A     H    25_A     17   34   38      4   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     I    26_A     I    26_A     17   34   38      4   13   17   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     I    27_A     I    27_A     17   34   38      4   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    28_A     K    28_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     C    29_A     C    29_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     H    30_A     H    30_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     F    31_A     F    31_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     D    32_A     D    32_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    33_A     K    33_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     C    34_A     C    34_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     N    35_A     N    35_A     17   34   38      4   14   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    36_A     K    36_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     S    37_A     S    37_A     17   34   38      5   15   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     Y    38_A     Y    38_A     17   34   38      4   15   19   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     N    39_A     N    39_A     17   34   38      3   15   17   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     W    40_A     W    40_A     17   34   38      4   15   17   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     R    41_A     R    41_A     13   34   38      3    6   12   23   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    42_A     K    42_A      7   34   38      3    6    9   14   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    43_A     K    43_A      7   34   38      4   11   17   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     Y    44_A     Y    44_A      7   34   38      4   11   16   23   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     G    45_A     G    45_A     13   34   38      4    9   22   25   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     K    46_A     K    46_A     13   34   38      8   10   12   24   28   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     L    47_A     L    47_A     13   34   38      8   11   22   25   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     R    48_A     R    48_A     13   34   38      8   13   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     L    49_A     L    49_A     13   34   38      8   10   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     V    50_A     V    50_A     13   34   38      8   11   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     D    51_A     D    51_A     13   34   38      8   13   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     H    52_A     H    52_A     13   34   38      8   13   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     A    53_A     A    53_A     13   34   38      8   11   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     F    54_A     F    54_A     13   34   38      7   13   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     T    55_A     T    55_A     13   34   38      4   10   22   26   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     H    56_A     H    56_A     13   34   38      4    9   12   22   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     V    57_A     V    57_A     13   34   38      4    7   12   20   30   34   34   34   34   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     P    58_A     P    58_A      4   14   38      3    4    5    5    6   13   17   25   31   35   35   35   35   36   37   39   42   45   46   47 
LCS_GDT     H    59_A     H    59_A      4    6   38      3    4    5    7    9   13   15   18   20   26   29   34   35   36   37   39   42   45   46   47 
LCS_GDT     L    60_A     L    60_A      4    6   38      4    6    6    7    9   10   15   18   20   24   28   30   32   33   37   39   42   45   46   47 
LCS_GDT     K    61_A     K    61_A      4    6   38      4    4    5    5    8   11   15   18   20   24   28   30   32   33   35   37   39   44   46   47 
LCS_GDT     M    62_A     M    62_A      4    7   32      4    4    5    5    6    9   14   16   20   22   27   30   32   33   35   36   37   39   42   47 
LCS_GDT     K    63_A     K    63_A      5    7   32      5    5    5    5    6   10   15   16   20   22   26   29   32   33   35   36   37   39   40   45 
LCS_GDT     C    64_A     C    64_A      5    7   32      5    5    5    6    8   11   15   18   20   24   28   30   32   33   35   36   37   39   42   47 
LCS_GDT     N    65_A     N    65_A      5    8   32      5    5    5    6    8   10   14   18   20   24   28   30   32   33   35   36   37   39   42   47 
LCS_GDT     F    66_A     F    66_A      5    9   32      5    5    5    7    8    8   14   16   19   24   28   30   32   33   35   36   37   39   42   47 
LCS_GDT     C    67_A     C    67_A      7   20   32      5    6    8   14   17   18   20   20   20   20   20   26   32   33   35   36   37   39   40   41 
LCS_GDT     D    68_A     D    68_A      9   20   32      4    7   11   15   17   18   20   20   20   21   28   30   32   33   35   36   37   39   42   47 
LCS_GDT     Y    69_A     Y    69_A      9   20   32      4    6   11   12   17   18   20   20   20   24   28   30   32   33   35   36   37   40   43   47 
LCS_GDT     M    70_A     M    70_A      9   20   32      4    6   11   15   17   18   20   20   20   24   28   30   32   33   35   38   41   45   46   47 
LCS_GDT     C    71_A     C    71_A     14   20   32      3    7   13   16   17   18   20   20   20   20   23   26   27   33   35   38   41   45   46   47 
LCS_GDT     K    72_A     K    72_A     15   20   31      3    7   13   16   17   18   20   20   20   20   20   21   22   22   22   23   24   26   40   44 
LCS_GDT     G    73_A     G    73_A     15   20   24      7   11   13   16   17   18   20   20   20   20   20   21   22   22   22   24   26   29   31   41 
LCS_GDT     I    74_A     I    74_A     15   20   24      8   11   13   16   17   18   20   20   20   20   20   21   22   22   24   32   42   45   46   47 
LCS_GDT     R    75_A     R    75_A     15   20   24      9   11   13   16   17   18   20   20   20   20   20   23   25   30   35   38   42   45   46   47 
LCS_GDT     N    76_A     N    76_A     15   20   24      9   11   13   16   17   18   20   20   20   24   28   30   31   33   35   38   42   45   46   47 
LCS_GDT     I    77_A     I    77_A     15   20   24      9   11   13   16   17   18   20   20   20   24   28   30   31   33   35   39   42   45   46   47 
LCS_GDT     R    78_A     R    78_A     15   20   24      9   11   13   16   17   18   20   20   20   20   22   26   29   33   35   39   42   45   46   47 
LCS_GDT     L    79_A     L    79_A     15   20   24      9   11   13   16   17   18   20   20   20   24   28   30   32   33   35   38   41   45   46   47 
LCS_GDT     H    80_A     H    80_A     15   20   24      9   11   13   16   17   18   20   20   20   24   28   30   32   33   35   36   38   40   45   47 
LCS_GDT     H    81_A     H    81_A     15   20   24      9   11   13   16   17   18   20   20   20   20   20   21   22   24   34   36   37   39   42   47 
LCS_GDT     K    82_A     K    82_A     15   20   24      9   11   13   16   17   18   20   20   20   20   20   21   22   23   26   36   37   38   41   47 
LCS_GDT     K    83_A     K    83_A     15   20   24      9   11   13   16   17   18   20   20   20   20   20   21   22   22   26   34   37   39   40   43 
LCS_GDT     S    84_A     S    84_A     15   20   24      6   11   13   16   16   18   20   20   20   20   20   21   22   22   22   23   24   26   28   35 
LCS_GDT     H    85_A     H    85_A     15   20   24      4    6   13   16   16   18   20   20   20   20   20   21   22   22   22   23   23   25   28   28 
LCS_GDT     P    86_A     P    86_A     15   20   24      4    6   12   16   16   18   20   20   20   20   20   21   22   22   22   23   24   26   28   29 
LCS_AVERAGE  LCS_A:  22.99  (  12.17   24.58   32.21 )

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      9     15     22     26     30     34     34     34     34     35     35     35     35     36     37     39     42     45     46     47 
GDT PERCENT_AT   8.57  14.29  20.95  24.76  28.57  32.38  32.38  32.38  32.38  33.33  33.33  33.33  33.33  34.29  35.24  37.14  40.00  42.86  43.81  44.76
GDT RMS_LOCAL    0.22   0.70   1.03   1.32   1.55   1.78   1.78   1.78   1.78   2.22   2.22   2.22   2.22   2.92   3.65   4.84   5.60   6.14   6.28   6.49
GDT RMS_ALL_AT  26.32  16.26  18.64  18.52  18.36  18.46  18.46  18.46  18.46  18.09  18.09  18.09  18.09  17.36  16.48  14.08  12.61  11.29  11.06  10.72

# Checking swapping
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  Y    69_A      Y    69_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    24_A      V    24_A     1.082     0    0.017   0.091     2.776   73.214   70.816
LGA    H    25_A      H    25_A     1.381     0    0.029   1.228     8.646   83.690   47.571
LGA    I    26_A      I    26_A     1.837     0    0.000   1.572     5.962   70.833   56.012
LGA    I    27_A      I    27_A     0.899     0    0.123   0.199     1.791   83.810   82.679
LGA    K    28_A      K    28_A     0.851     0    0.130   0.714     4.323   85.952   70.741
LGA    C    29_A      C    29_A     0.630     0    0.034   0.182     0.685   95.238   93.651
LGA    H    30_A      H    30_A     0.782     0    0.286   0.406     1.645   86.071   85.095
LGA    F    31_A      F    31_A     1.004     0    0.039   0.969     7.075   88.333   55.498
LGA    D    32_A      D    32_A     0.627     0    0.108   0.604     1.993   92.857   86.131
LGA    K    33_A      K    33_A     0.974     0    0.055   0.797     1.849   85.952   84.550
LGA    C    34_A      C    34_A     1.556     0    0.258   0.291     2.360   72.976   71.587
LGA    N    35_A      N    35_A     1.355     0    0.314   0.894     3.738   79.286   70.476
LGA    K    36_A      K    36_A     1.255     0    0.126   0.769     4.716   79.286   63.228
LGA    S    37_A      S    37_A     0.655     0    0.182   0.672     2.550   90.476   84.921
LGA    Y    38_A      Y    38_A     1.503     0    0.049   0.184     2.430   70.952   74.444
LGA    N    39_A      N    39_A     2.225     0    0.079   1.106     5.322   64.762   51.667
LGA    W    40_A      W    40_A     2.053     0    0.098   1.110     5.303   66.786   51.565
LGA    R    41_A      R    41_A     2.907     0    0.047   1.181    10.522   69.048   34.329
LGA    K    42_A      K    42_A     2.934     0    0.179   0.737    12.260   57.262   32.540
LGA    K    43_A      K    43_A     1.939     0    0.083   0.928     3.038   66.786   68.624
LGA    Y    44_A      Y    44_A     2.850     0    0.206   0.998    11.285   62.976   30.238
LGA    G    45_A      G    45_A     2.304     0    0.243   0.243     2.304   73.214   73.214
LGA    K    46_A      K    46_A     2.933     0    0.063   0.717     3.589   57.143   53.333
LGA    L    47_A      L    47_A     2.136     0    0.068   0.147     2.507   68.810   65.833
LGA    R    48_A      R    48_A     1.241     0    0.035   1.113     5.614   79.286   61.385
LGA    L    49_A      L    49_A     1.822     0    0.000   1.449     5.010   75.000   62.262
LGA    V    50_A      V    50_A     1.649     0    0.027   0.034     2.595   77.143   70.748
LGA    D    51_A      D    51_A     0.909     0    0.088   0.230     2.429   88.214   79.583
LGA    H    52_A      H    52_A     0.836     0    0.021   0.417     3.524   88.214   70.667
LGA    A    53_A      A    53_A     1.287     0    0.017   0.037     1.722   85.952   83.333
LGA    F    54_A      F    54_A     1.241     0    0.095   1.008     3.131   81.429   78.095
LGA    T    55_A      T    55_A     1.734     0    0.078   0.150     2.876   75.000   68.435
LGA    H    56_A      H    56_A     2.744     0    0.128   1.227     4.967   57.619   50.857
LGA    V    57_A      V    57_A     2.890     0    0.260   0.231     5.635   43.690   48.435
LGA    P    58_A      P    58_A     8.333     0    0.080   0.129     9.793    5.952    5.782
LGA    H    59_A      H    59_A    13.117     0    0.070   0.240    16.199    0.000    0.048
LGA    L    60_A      L    60_A    16.416     0    0.132   0.839    19.780    0.000    0.000
LGA    K    61_A      K    61_A    21.165     0    0.138   0.932    24.094    0.000    0.000
LGA    M    62_A      M    62_A    26.491     0    0.032   1.112    28.382    0.000    0.000
LGA    K    63_A      K    63_A    32.152     0    0.647   1.189    34.424    0.000    0.000
LGA    C    64_A      C    64_A    33.123     0    0.043   0.117    35.818    0.000    0.000
LGA    N    65_A      N    65_A    36.781     0    0.186   0.217    39.427    0.000    0.000
LGA    F    66_A      F    66_A    38.192     0    0.600   0.413    39.645    0.000    0.000
LGA    C    67_A      C    67_A    37.619     0    0.142   0.681    39.175    0.000    0.000
LGA    D    68_A      D    68_A    34.179     0    0.061   0.939    37.021    0.000    0.000
LGA    Y    69_A      Y    69_A    32.880     0    0.084   0.087    36.267    0.000    0.000
LGA    M    70_A      M    70_A    26.844     0    0.081   0.755    29.296    0.000    0.000
LGA    C    71_A      C    71_A    24.751     0    0.125   0.647    25.398    0.000    0.000
LGA    K    72_A      K    72_A    21.815     0    0.621   0.802    26.338    0.000    0.000
LGA    G    73_A      G    73_A    20.023     0    0.179   0.179    20.344    0.000    0.000
LGA    I    74_A      I    74_A    17.041     0    0.030   0.115    17.820    0.000    0.000
LGA    R    75_A      R    75_A    19.482     0    0.015   1.063    30.809    0.000    0.000
LGA    N    76_A      N    76_A    23.132     0    0.000   0.255    26.545    0.000    0.000
LGA    I    77_A      I    77_A    21.008     0    0.096   1.255    22.060    0.000    0.000
LGA    R    78_A      R    78_A    19.321     0    0.000   0.956    21.636    0.000    0.433
LGA    L    79_A      L    79_A    24.037     0    0.065   1.391    28.011    0.000    0.000
LGA    H    80_A      H    80_A    27.483     0    0.047   0.196    32.690    0.000    0.000
LGA    H    81_A      H    81_A    25.538     0    0.025   1.582    27.619    0.000    0.000
LGA    K    82_A      K    82_A    25.719     0    0.060   1.001    29.321    0.000    0.000
LGA    K    83_A      K    83_A    31.889     0    0.000   0.943    35.859    0.000    0.000
LGA    S    84_A      S    84_A    33.992     0    0.055   0.651    35.652    0.000    0.000
LGA    H    85_A      H    85_A    31.888     0    0.064   1.483    31.888    0.000    0.000
LGA    P    86_A      P    86_A    31.965     0    0.575   0.514    35.799    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     539    539  100.00               105
SUMMARY(RMSD_GDC):     9.216          9.220                  9.965           24.602   21.322

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  105    4.0     34    1.78    27.143    27.945     1.809

LGA_LOCAL      RMSD:   1.779  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.457  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   9.216  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.809698 * X  +   0.580621 * Y  +   0.085249 * Z  + -353.063507
  Y_new =   0.512047 * X  +  -0.769969 * Y  +   0.380729 * Z  + -20.177919
  Z_new =   0.286698 * X  +  -0.264625 * Y  +  -0.920749 * Z  + 249.620163 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.563898 -0.290779 -2.861734   [DEG:   32.3090  -16.6604 -163.9653 ]
ZXZ:  2.921317  2.740791  2.316178   [DEG:  167.3792  157.0358  132.7072 ]
 
# END of job
