
#######################################################
#                                                     #
#                        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   68 (  570),  selected   68 , name one
# Molecule2: number of CA atoms  312 ( 2500),  selected   68 , 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:    42      23_A - 64_A        4.70    11.91
  LCS_AVERAGE:     12.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      67_A - 90_A        1.67    19.90
  LCS_AVERAGE:      5.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      68_A - 89_A        0.82    19.94
  LCS_AVERAGE:      4.47

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   68
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     P    23_A     P    23_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Q    24_A     Q    24_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     G    25_A     G    25_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     N    26_A     N    26_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     F    27_A     F    27_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     E    28_A     E    28_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Q    29_A     Q    29_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     L    30_A     L    30_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     W    31_A     W    31_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     K    32_A     K    32_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     I    33_A     I    33_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     I    34_A     I    34_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     D    35_A     D    35_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     E    36_A     E    36_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Q    37_A     Q    37_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Y    38_A     Y    38_A     18   23   42     16   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     C    39_A     C    39_A     18   23   42      3   17   19   21   22   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     F    40_A     F    40_A     18   23   42      4   17   19   21   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     L    41_A     L    41_A      7   23   42      4    7   12   19   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     D    42_A     D    42_A      7   23   42      3    5    9   10   15   21   24   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Y    43_A     Y    43_A      7   23   42      4    7   12   19   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     K    44_A     K    44_A      7   23   42      4    6   10   16   20   23   26   29   34   35   37   40   41   42   43   44   45   46   48   50 
LCS_GDT     Q    45_A     Q    45_A      7   23   42      3    5    7    7    9   11   23   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     I    46_A     I    46_A      7    9   42      3    6    8   12   21   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     D    47_A     D    47_A      7    9   42      5   17   18   21   23   25   26   29   31   34   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     W    48_A     W    48_A      7    9   42      5    6   19   20   23   25   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     D    49_A     D    49_A      7    9   42      5    6    7   11   15   23   24   27   30   31   34   35   38   42   43   44   45   46   48   50 
LCS_GDT     E    50_A     E    50_A      7    9   42      5    6    8   12   15   18   24   27   30   31   34   36   38   42   43   44   45   46   48   50 
LCS_GDT     I    51_A     I    51_A      7    9   42      5    7   11   21   23   25   26   29   30   33   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     H    52_A     H    52_A      6    9   42      1    5   11   21   23   25   25   29   30   33   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     T    53_A     T    53_A      3    4   42      3    3    4    7    9   11   22   29   30   33   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     R    54_A     R    54_A      3    4   42      3    3    4    8   18   22   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Y    55_A     Y    55_A      3    4   42      3    3    3    4    7    7   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     Q    56_A     Q    56_A      3    4   42      3    3    3    4    5    7   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     K    57_A     K    57_A      3    4   42      3    3    3    4    6   15   26   27   32   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     L    58_A     L    58_A      3    6   42      3    3    4    6    7   11   12   14   17   23   25   27   36   40   42   44   44   46   48   50 
LCS_GDT     I    59_A     I    59_A      4    6   42      3    4    4    4    5   10   10   13   15   19   25   36   38   40   42   44   45   46   48   50 
LCS_GDT     T    60_A     T    60_A      4    6   42      3    4    4    6    7   22   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     P    61_A     P    61_A      4    6   42      3    4   10   16   20   23   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     N    62_A     N    62_A      4    6   42      3    4    4    5    8   12   18   23   31   35   36   38   41   42   43   44   45   46   48   50 
LCS_GDT     M    63_A     M    63_A      4    6   42      3    4    4    5   16   20   24   29   34   35   37   40   41   42   43   44   45   46   48   50 
LCS_GDT     G    64_A     G    64_A      4    6   42      3    4    5    6    7   11   12   15   23   25   27   32   36   39   43   43   44   46   48   50 
LCS_GDT     S    65_A     S    65_A      3    6   34      3    4    5    6   10   13   19   23   24   26   26   27   28   31   35   39   40   44   48   50 
LCS_GDT     E    66_A     E    66_A      3    5   34      3    3    5    6    7   11   15   21   24   26   26   27   28   31   34   35   39   41   44   50 
LCS_GDT     G    67_A     G    67_A      3   24   34      3    3    4    4   10   15   24   24   24   26   26   27   28   30   34   36   39   43   47   50 
LCS_GDT     L    68_A     L    68_A     22   24   34      3    3   21   22   23   23   24   24   24   26   26   27   28   34   36   39   44   46   48   50 
LCS_GDT     F    69_A     F    69_A     22   24   34     11   19   21   22   23   23   24   24   24   26   27   35   38   39   43   43   44   46   48   50 
LCS_GDT     E    70_A     E    70_A     22   24   34     11   19   21   22   23   23   24   24   24   32   36   39   41   42   43   44   45   46   48   50 
LCS_GDT     V    71_A     V    71_A     22   24   34      8   19   21   22   23   23   26   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     L    72_A     L    72_A     22   24   34     10   19   21   22   23   23   24   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     S    73_A     S    73_A     22   24   34     11   19   21   22   23   23   24   29   34   35   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     E    74_A     E    74_A     22   24   34     11   19   21   22   23   23   25   29   31   34   38   40   41   42   43   44   45   46   48   50 
LCS_GDT     M    75_A     M    75_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   31   39   45   46   48   50 
LCS_GDT     L    76_A     L    76_A     22   24   34     10   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   36   44   48   50 
LCS_GDT     Y    77_A     Y    77_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   36   43   48   50 
LCS_GDT     E    78_A     E    78_A     22   24   34      9   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   37   38 
LCS_GDT     L    79_A     L    79_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   34   36 
LCS_GDT     Q    80_A     Q    80_A     22   24   34      5   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   35   37 
LCS_GDT     D    81_A     D    81_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   34   37 
LCS_GDT     G    82_A     G    82_A     22   24   34      8   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   34   37   39   42 
LCS_GDT     H    83_A     H    83_A     22   24   34      5   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   35   37 
LCS_GDT     V    84_A     V    84_A     22   24   34      8   19   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   36   38 
LCS_GDT     N    85_A     N    85_A     22   24   34      3    6   20   22   23   23   24   24   24   26   26   27   28   29   31   32   36   42   44   49 
LCS_GDT     L    86_A     L    86_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   34   35   43   46   48   50 
LCS_GDT     A    87_A     A    87_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   29   34   35   40   43   47   50 
LCS_GDT     S    88_A     S    88_A     22   24   34     11   19   21   22   23   23   24   24   24   26   26   27   28   31   34   35   40   41   44   50 
LCS_GDT     A    89_A     A    89_A     22   24   34      4   12   21   22   23   23   24   24   24   26   26   27   28   29   31   32   33   34   44   45 
LCS_GDT     H    90_A     H    90_A      6   24   34      4    5    8    9   23   23   24   24   24   26   26   27   28   31   34   35   38   40   44   45 
LCS_AVERAGE  LCS_A:   7.60  (   4.47    5.85   12.48 )

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     16     19     21     22     23     25     26     29     34     35     38     40     41     42     43     44     45     46     48     50 
GDT PERCENT_AT   5.13   6.09   6.73   7.05   7.37   8.01   8.33   9.29  10.90  11.22  12.18  12.82  13.14  13.46  13.78  14.10  14.42  14.74  15.38  16.03
GDT RMS_LOCAL    0.24   0.48   0.76   0.82   1.07   1.65   1.88   2.43   2.90   2.97   3.39   3.52   3.64   3.76   3.93   4.11   4.28   4.46   4.88   6.19
GDT RMS_ALL_AT  13.91  20.02  19.95  19.94  19.84  14.24  13.36  12.09  11.65  11.65  12.13  12.01  11.99  11.91  11.99  12.12  12.08  12.09  12.00  11.37

# Checking swapping
#   possible swapping detected:  E    28_A      E    28_A
#   possible swapping detected:  D    35_A      D    35_A
#   possible swapping detected:  E    36_A      E    36_A
#   possible swapping detected:  D    42_A      D    42_A
#   possible swapping detected:  D    47_A      D    47_A
#   possible swapping detected:  E    66_A      E    66_A
#   possible swapping detected:  F    69_A      F    69_A
#   possible swapping detected:  E    70_A      E    70_A
#   possible swapping detected:  E    78_A      E    78_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P    23_A      P    23_A     1.904     0    0.094   0.094     2.266   72.857   69.388
LGA    Q    24_A      Q    24_A     0.977     0    0.035   1.414     7.088   88.214   62.381
LGA    G    25_A      G    25_A     1.075     0    0.087   0.087     1.130   83.690   83.690
LGA    N    26_A      N    26_A     1.486     0    0.032   0.574     2.802   81.429   75.179
LGA    F    27_A      F    27_A     0.922     0    0.052   1.190     8.683   92.976   52.208
LGA    E    28_A      E    28_A     0.113     0    0.042   0.919     3.170  100.000   81.852
LGA    Q    29_A      Q    29_A     0.652     0    0.032   1.210     3.187   92.857   80.265
LGA    L    30_A      L    30_A     0.183     0    0.034   1.395     3.816   97.619   79.286
LGA    W    31_A      W    31_A     0.473     0    0.080   0.422     1.985   95.238   88.810
LGA    K    32_A      K    32_A     0.936     0    0.015   0.094     2.470   85.952   79.788
LGA    I    33_A      I    33_A     1.112     0    0.020   0.552     1.572   81.548   82.679
LGA    I    34_A      I    34_A     1.460     0    0.029   0.702     3.436   75.119   73.274
LGA    D    35_A      D    35_A     1.851     0    0.128   0.203     3.267   70.833   64.048
LGA    E    36_A      E    36_A     2.093     0    0.025   0.059     2.476   66.786   65.661
LGA    Q    37_A      Q    37_A     1.708     0    0.091   0.501     3.909   72.857   69.683
LGA    Y    38_A      Y    38_A     1.644     0    0.037   0.076     1.752   72.857   72.857
LGA    C    39_A      C    39_A     2.204     0    0.147   0.749     3.467   72.976   67.778
LGA    F    40_A      F    40_A     1.240     0    0.123   0.548     6.399   81.548   53.896
LGA    L    41_A      L    41_A     2.141     0    0.039   1.240     6.351   60.595   54.881
LGA    D    42_A      D    42_A     4.365     0    0.017   0.282     8.309   39.167   27.024
LGA    Y    43_A      Y    43_A     2.475     0    0.033   1.345     4.996   51.071   52.143
LGA    K    44_A      K    44_A     4.634     0    0.148   0.332     8.424   31.905   25.238
LGA    Q    45_A      Q    45_A     5.004     0    0.398   0.877    12.485   35.952   17.619
LGA    I    46_A      I    46_A     2.832     0    0.088   1.290     6.280   59.524   47.679
LGA    D    47_A      D    47_A     2.583     0    0.068   0.117     6.166   62.857   46.845
LGA    W    48_A      W    48_A     2.468     0    0.063   1.617    11.421   59.167   28.435
LGA    D    49_A      D    49_A     5.822     0    0.021   0.099     9.054   22.857   14.643
LGA    E    50_A      E    50_A     6.161     0    0.033   1.124     7.595   20.476   18.095
LGA    I    51_A      I    51_A     3.285     0    0.329   0.621     3.890   48.333   54.643
LGA    H    52_A      H    52_A     3.728     0    0.510   1.120     9.833   50.119   25.476
LGA    T    53_A      T    53_A     5.340     0    0.553   1.195     9.783   33.214   21.905
LGA    R    54_A      R    54_A     6.101     0    0.083   1.313    11.888   14.881    9.437
LGA    Y    55_A      Y    55_A     8.088     0    0.675   0.897    19.442    8.095    2.937
LGA    Q    56_A      Q    56_A     7.527     0    0.044   1.268     9.052    7.857    7.249
LGA    K    57_A      K    57_A     7.581     0    0.462   1.059    10.758    4.762    3.598
LGA    L    58_A      L    58_A    12.625     0    0.620   0.566    19.175    0.000    0.000
LGA    I    59_A      I    59_A    10.620     0    0.541   1.342    16.327    1.429    0.714
LGA    T    60_A      T    60_A     6.682     0    0.044   0.122     9.681   17.619   11.565
LGA    P    61_A      P    61_A     3.451     0    0.329   0.487     4.938   39.048   41.837
LGA    N    62_A      N    62_A     8.859     0    0.504   0.924    13.614    5.952    2.976
LGA    M    63_A      M    63_A     7.763     0    0.678   1.022    11.179    3.571   15.655
LGA    G    64_A      G    64_A    14.777     0    0.078   0.078    15.167    0.000    0.000
LGA    S    65_A      S    65_A    18.073     0    0.623   0.752    19.586    0.000    0.000
LGA    E    66_A      E    66_A    21.624     0    0.423   0.411    28.816    0.000    0.000
LGA    G    67_A      G    67_A    18.538     0    0.039   0.039    19.356    0.000    0.000
LGA    L    68_A      L    68_A    13.761     0    0.573   0.694    15.643    0.000    0.060
LGA    F    69_A      F    69_A    13.613     0    0.050   1.198    21.269    0.000    0.000
LGA    E    70_A      E    70_A     8.371     0    0.060   1.208    10.462   17.381    8.783
LGA    V    71_A      V    71_A     3.167     0    0.046   0.349     5.624   44.048   43.673
LGA    L    72_A      L    72_A     7.589     0    0.070   0.981    13.357    8.452    4.226
LGA    S    73_A      S    73_A     8.500     0    0.032   0.651     9.115    5.119    4.127
LGA    E    74_A      E    74_A     4.806     0    0.093   0.894     9.235   18.571   21.058
LGA    M    75_A      M    75_A     9.982     0    0.022   0.676    14.463    1.905    1.071
LGA    L    76_A      L    76_A    14.857     0    0.044   0.092    18.122    0.000    0.000
LGA    Y    77_A      Y    77_A    13.074     0    0.065   1.581    16.453    0.000    2.817
LGA    E    78_A      E    78_A    17.454     0    0.026   0.982    22.166    0.000    0.000
LGA    L    79_A      L    79_A    23.077     0    0.047   0.054    26.273    0.000    0.000
LGA    Q    80_A      Q    80_A    22.455     0    0.147   0.990    26.004    0.000    0.000
LGA    D    81_A      D    81_A    25.779     0    0.044   0.071    31.554    0.000    0.000
LGA    G    82_A      G    82_A    24.403     0    0.007   0.007    26.195    0.000    0.000
LGA    H    83_A      H    83_A    30.018     0    0.228   0.185    35.689    0.000    0.000
LGA    V    84_A      V    84_A    26.018     0    0.144   0.142    27.622    0.000    0.000
LGA    N    85_A      N    85_A    23.583     0    0.152   0.854    27.770    0.000    0.000
LGA    L    86_A      L    86_A    21.734     0    0.045   0.149    22.911    0.000    0.000
LGA    A    87_A      A    87_A    26.617     0    0.059   0.065    29.477    0.000    0.000
LGA    S    88_A      S    88_A    27.358     0    0.033   0.065    31.480    0.000    0.000
LGA    A    89_A      A    89_A    33.654     0    0.041   0.053    36.464    0.000    0.000
LGA    H    90_A      H    90_A    33.306     0    0.695   1.049    33.306    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       68     272    272  100.00     570    570  100.00               312
SUMMARY(RMSD_GDC):    10.284         10.261                 10.847            7.241    6.151

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  312    4.0     29    2.29     9.135     8.523     1.213

LGA_LOCAL      RMSD:   2.291  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.450  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:  10.284  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.710378 * X  +  -0.364831 * Y  +  -0.601882 * Z  +  10.188624
  Y_new =  -0.294631 * X  +  -0.622481 * Y  +   0.725059 * Z  +  21.457109
  Z_new =  -0.639184 * X  +   0.692398 * Y  +   0.334706 * Z  +  28.285971 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.748434  0.693437  1.120516   [DEG: -157.4737   39.7310   64.2008 ]
ZXZ: -2.448757  1.229503 -0.745456   [DEG: -140.3034   70.4453  -42.7115 ]
 
# END of job
