
#######################################################
#                                                     #
#                        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   69 (  613),  selected   64 , name one
# Molecule2: number of CA atoms   76 (  680),  selected   64 , 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:    45      16_B - 65_B        4.06     7.94
  LCS_AVERAGE:     47.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43      16_B - 58_B        1.71     8.66
  LCS_AVERAGE:     40.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34      20_B - 53_B        1.00     8.45
  LCS_AVERAGE:     30.35

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     K    16_B     K    16_B     31   43   45      7   15   24   34   41   45   45   46   47   47   49   49   51   52   53   53   53   54   55   56 
LCS_GDT     K    17_B     K    17_B     33   43   45     12   21   31   39   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    18_B     K    18_B     33   43   45     12   21   33   39   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    19_B     L    19_B     33   43   45     12   23   35   40   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    20_B     E    20_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    21_B     E    21_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    22_B     E    22_B     34   43   45     10   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    23_B     L    23_B     34   43   45     10   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    24_B     K    24_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    25_B     K    25_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     I    26_B     I    26_B     34   43   45     12   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     R    27_B     R    27_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    28_B     E    28_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     R    29_B     R    29_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    30_B     L    30_B     34   43   45     11   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    31_B     L    31_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     M    32_B     M    32_B     34   43   45      3   21   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     V    33_B     V    33_B     34   43   45      9   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     F    34_B     F    34_B     34   43   45      9   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     D    35_B     D    35_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    36_B     E    36_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    37_B     E    37_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     R    38_B     R    38_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     V    39_B     V    39_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    40_B     E    40_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    41_B     E    41_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     Y    42_B     Y    42_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     M    43_B     M    43_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    44_B     K    44_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     I    45_B     I    45_B     34   43   45     11   23   34   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     M    46_B     M    46_B     34   43   45     12   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    47_B     K    47_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    48_B     E    48_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     V    49_B     V    49_B     34   43   45     17   23   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     I    50_B     I    50_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    51_B     E    51_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    52_B     K    52_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     I    53_B     I    53_B     34   43   45     17   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    54_B     L    54_B     29   43   45     11   22   32   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    55_B     E    55_B     28   43   45     12   22   32   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     N    56_B     N    56_B     28   43   45     10   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     R    57_B     R    57_B     28   43   45      5   22   35   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     K    58_B     K    58_B      3   43   45      3    3    3    3    3   24   27   31   40   47   49   49   51   52   53   53   53   54   55   56 
LCS_GDT     K    64_B     K    64_B      4    4   45      3    4    4    4    4    5    5    8   11   14   14   18   25   34   42   48   49   52   53   54 
LCS_GDT     V    65_B     V    65_B      4    5   45      3    4    4    4    6    7    8    9   11   14   14   15   17   17   19   21   21   22   23   28 
LCS_GDT     E    66_B     E    66_B      4    6   28      3    4    4    4    6    7    8    9   11   14   14   15   17   17   19   21   24   27   32   37 
LCS_GDT     I    67_B     I    67_B      4    6   15      3    4    4    4    4    7    7    9   11   14   14   15   17   18   19   21   26   30   32   37 
LCS_GDT     P    68_B     P    68_B      4    6   15      3    4    4    5    6    7    8    9   11   14   14   15   17   19   24   27   32   36   39   42 
LCS_GDT     P    69_B     P    69_B      4    6   15      3    4    4    5    6    7    8    9   11   14   14   15   17   19   24   27   32   36   39   42 
LCS_GDT     G    70_B     G    70_B      4    6   15      3    4    4    5    5    7    8    9   11   14   14   15   17   18   19   22   24   32   36   42 
LCS_GDT     M    71_B     M    71_B      3    6   15      3    4    4    5    5    7    7    8   11   14   14   15   17   18   19   26   32   36   39   44 
LCS_GDT     E    72_B     E    72_B      3    5   15      3    4    4    5    6    7    8    9   11   22   37   44   48   48   50   53   53   54   55   56 
LCS_GDT     W    73_B     W    73_B      3    5   15      1    4    4    5    6    7    8    9   11   43   44   49   49   51   52   53   53   54   55   56 
LCS_GDT     F    74_B     F    74_B      3    4   15      0   10   18   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     Y    75_B     Y    75_B      4    5   15      3    4    4   12   16   22   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     E    76_B     E    76_B      4    5   15      3    3    4    4    5    5    7   12   16   19   41   43   46   51   53   53   53   54   54   56 
LCS_GDT     N    77_B     N    77_B      4    5   15      3    3    4    6    6    6    8   10   31   37   41   50   50   52   53   53   53   54   55   56 
LCS_GDT     F    78_B     F    78_B      4    5   15      3    4    4    6    6    6    8   12   31   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     L    79_B     L    79_B      3    5   14      3    3    3    6    6    6    8   27   31   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     R    80_B     R    80_B      3    3   11      3    3    3    3    8    9   10   36   40   47   48   50   51   52   53   53   53   54   55   56 
LCS_GDT     Y    81_B     Y    81_B      3    3   11      3   14   33   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     Y    82_B     Y    82_B      3    3   11      5   19   34   41   44   45   45   46   47   47   49   50   51   52   53   53   53   54   55   56 
LCS_GDT     D    83_B     D    83_B      3    3   11      0    9   17   25   35   42   45   45   47   47   48   50   51   52   53   53   53   54   55   56 
LCS_GDT     Y    84_B     Y    84_B      3    3   11      0    4    5    5    5    5    6    6    6    6    8   14   46   48   49   50   53   54   55   56 
LCS_AVERAGE  LCS_A:  39.24  (  30.35   40.05   47.33 )

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     17     23     35     41     44     45     45     46     47     47     49     50     51     52     53     53     53     54     55     56 
GDT PERCENT_AT  22.37  30.26  46.05  53.95  57.89  59.21  59.21  60.53  61.84  61.84  64.47  65.79  67.11  68.42  69.74  69.74  69.74  71.05  72.37  73.68
GDT RMS_LOCAL    0.32   0.74   1.02   1.19   1.32   1.40   1.40   1.54   1.68   1.68   2.22   2.50   2.49   2.69   2.94   2.88   2.88   3.12   3.52   3.73
GDT RMS_ALL_AT   8.17   8.33   8.57   8.60   8.63   8.63   8.63   8.66   8.64   8.64   8.71   8.74   8.69   8.75   8.85   8.70   8.70   8.79   8.57   8.65

# Checking swapping
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  E    40_B      E    40_B
#   possible swapping detected:  E    48_B      E    48_B
#   possible swapping detected:  E    66_B      E    66_B
#   possible swapping detected:  F    74_B      F    74_B
#   possible swapping detected:  Y    75_B      Y    75_B
#   possible swapping detected:  Y    81_B      Y    81_B
#   possible swapping detected:  D    83_B      D    83_B
#   possible swapping detected:  Y    84_B      Y    84_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    16_B      K    16_B     3.196     0    0.662   0.556    12.356   61.429   31.799
LGA    K    17_B      K    17_B     2.298     0    0.051   1.014     3.443   64.881   67.937
LGA    K    18_B      K    18_B     2.184     0    0.032   0.089     2.633   68.810   64.868
LGA    L    19_B      L    19_B     1.501     0    0.028   1.407     4.786   79.405   62.798
LGA    E    20_B      E    20_B     1.240     0    0.025   0.409     3.877   85.952   73.704
LGA    E    21_B      E    21_B     1.166     0    0.026   0.968     4.487   85.952   70.423
LGA    E    22_B      E    22_B     0.654     0    0.033   0.903     3.358   92.857   82.222
LGA    L    23_B      L    23_B     0.640     0    0.031   1.294     3.685   92.857   81.310
LGA    K    24_B      K    24_B     0.514     0    0.021   1.133     5.327   95.238   78.201
LGA    K    25_B      K    25_B     0.712     0    0.022   0.597     1.803   90.476   84.550
LGA    I    26_B      I    26_B     0.869     0    0.030   0.051     1.181   88.214   88.214
LGA    R    27_B      R    27_B     0.674     0    0.014   1.033     3.679   90.476   84.545
LGA    E    28_B      E    28_B     0.373     0    0.047   0.865     3.443   95.238   78.042
LGA    R    29_B      R    29_B     0.902     0    0.040   1.339     7.783   88.214   59.221
LGA    L    30_B      L    30_B     0.979     0    0.037   0.144     1.219   85.952   87.083
LGA    L    31_B      L    31_B     1.239     0    0.196   0.989     2.692   79.286   75.179
LGA    M    32_B      M    32_B     1.522     0    0.185   0.653     2.200   77.143   73.988
LGA    V    33_B      V    33_B     0.743     0    0.042   0.109     0.775   90.476   90.476
LGA    F    34_B      F    34_B     0.232     0    0.694   0.771     2.816   86.905   80.390
LGA    D    35_B      D    35_B     1.302     0    0.055   0.824     3.005   83.810   73.571
LGA    E    36_B      E    36_B     0.855     0    0.037   0.678     3.340   90.476   79.153
LGA    E    37_B      E    37_B     1.136     0    0.056   1.181     4.031   83.690   69.418
LGA    R    38_B      R    38_B     1.348     0    0.040   1.311     6.068   81.429   66.320
LGA    V    39_B      V    39_B     0.853     0    0.034   0.977     3.380   90.476   79.728
LGA    E    40_B      E    40_B     0.768     0    0.033   1.013     4.033   90.476   75.344
LGA    E    41_B      E    41_B     1.514     0    0.057   0.157     3.102   79.286   67.143
LGA    Y    42_B      Y    42_B     1.340     0    0.020   0.459     2.541   81.429   75.238
LGA    M    43_B      M    43_B     0.385     0    0.020   0.176     2.001   97.619   89.821
LGA    K    44_B      K    44_B     1.090     0    0.033   1.053     4.320   83.690   72.910
LGA    I    45_B      I    45_B     1.796     0    0.041   0.056     3.256   79.286   68.274
LGA    M    46_B      M    46_B     1.284     0    0.051   1.184     3.213   83.690   76.488
LGA    K    47_B      K    47_B     0.818     0    0.081   0.874     7.377   92.857   61.852
LGA    E    48_B      E    48_B     1.019     0    0.072   0.733     2.736   88.214   77.937
LGA    V    49_B      V    49_B     0.828     0    0.038   0.318     2.821   90.476   81.905
LGA    I    50_B      I    50_B     1.428     0    0.021   0.095     2.091   79.286   75.060
LGA    E    51_B      E    51_B     1.450     0    0.023   0.265     1.698   79.286   79.524
LGA    K    52_B      K    52_B     0.806     0    0.044   0.986     7.462   92.857   67.143
LGA    I    53_B      I    53_B     1.066     0    0.021   0.103     3.045   86.071   73.631
LGA    L    54_B      L    54_B     2.508     0    0.059   1.371     7.516   62.976   44.583
LGA    E    55_B      E    55_B     2.406     0    0.067   0.386     4.529   66.786   54.709
LGA    N    56_B      N    56_B     1.365     0    0.467   1.008     5.292   69.762   60.655
LGA    R    57_B      R    57_B     1.385     0    0.055   1.272    10.863   59.405   37.143
LGA    K    58_B      K    58_B     7.692     0    0.235   0.322    15.115    8.690    4.074
LGA    K    64_B      K    64_B    18.368     0    0.646   0.750    22.057    0.000    0.000
LGA    V    65_B      V    65_B    22.366     0    0.486   0.969    24.034    0.000    0.000
LGA    E    66_B      E    66_B    25.531     0    0.660   0.494    33.397    0.000    0.000
LGA    I    67_B      I    67_B    24.358     0    0.657   0.609    25.193    0.000    0.000
LGA    P    68_B      P    68_B    23.263     0    0.061   0.345    23.311    0.000    0.000
LGA    P    69_B      P    69_B    25.041     0    0.650   0.554    26.496    0.000    0.000
LGA    G    70_B      G    70_B    22.131     0    0.730   0.730    22.585    0.000    0.000
LGA    M    71_B      M    71_B    16.150     0    0.608   1.257    19.665    0.000    0.000
LGA    E    72_B      E    72_B    10.804     0    0.592   0.865    12.957    2.500    1.111
LGA    W    73_B      W    73_B     7.314     0    0.653   1.606    14.681   19.405    5.612
LGA    F    74_B      F    74_B     2.182     0    0.614   0.952    10.353   59.881   28.788
LGA    Y    75_B      Y    75_B     4.564     0    0.595   1.416     8.025   28.571   20.675
LGA    E    76_B      E    76_B     9.926     0    0.337   0.542    15.662    2.024    0.899
LGA    N    77_B      N    77_B     8.491     0    0.261   0.557     9.829    3.810    2.917
LGA    F    78_B      F    78_B     6.892     0    0.593   1.447    12.985   10.952    5.584
LGA    L    79_B      L    79_B     6.580     0    0.615   0.631     9.848   12.738    8.393
LGA    R    80_B      R    80_B     6.460     0    0.611   0.831    17.055   25.238    9.610
LGA    Y    81_B      Y    81_B     2.122     0    0.614   1.417     9.596   57.381   41.230
LGA    Y    82_B      Y    82_B     1.862     0    0.571   1.330     7.244   68.810   52.817
LGA    D    83_B      D    83_B     5.002     0    0.583   1.312     9.203   20.119   14.881
LGA    Y    84_B      Y    84_B    11.269     0    0.593   1.474    23.384    0.714    0.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     576    576  100.00                76
SUMMARY(RMSD_GDC):     7.609          7.607                  8.386           50.183   42.360

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   69   76    4.0     46    1.54    53.618    52.649     2.800

LGA_LOCAL      RMSD:   1.543  Number of atoms:   46  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.656  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   7.609  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.583602 * X  +  -0.811290 * Y  +  -0.034880 * Z  +  10.391975
  Y_new =   0.391591 * X  +   0.318801 * Y  +  -0.863147 * Z  +   4.134613
  Z_new =   0.711382 * X  +   0.490076 * Y  +   0.503747 * Z  +  18.929306 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.590989 -0.791463  0.771643   [DEG:   33.8612  -45.3475   44.2119 ]
ZXZ: -0.040388  1.042866  0.967555   [DEG:   -2.3141   59.7518   55.4368 ]
 
# END of job
