
#######################################################
#                                                     #
#                        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 (  550),  selected   69 , name one
# Molecule2: number of CA atoms  443 ( 3614),  selected   69 , 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:    20     184_A - 203_A       4.97    22.35
  LONGEST_CONTINUOUS_SEGMENT:    20     185_A - 204_A       4.85    23.26
  LCS_AVERAGE:      3.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8     160_A - 167_A       1.92    22.97
  LONGEST_CONTINUOUS_SEGMENT:     8     161_A - 168_A       1.88    23.18
  LONGEST_CONTINUOUS_SEGMENT:     8     180_A - 187_A       1.67    17.30
  LONGEST_CONTINUOUS_SEGMENT:     8     181_A - 188_A       1.86    17.68
  LCS_AVERAGE:      1.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7     150_A - 156_A       0.94    25.53
  LCS_AVERAGE:      1.01

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   69
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     N   146_A     N   146_A      5    6   16      3    4    5    6    7    8    8   10   11   12   15   16   17   20   26   28   30   32   35   37 
LCS_GDT     I   147_A     I   147_A      5    6   16      3    4    5    6    7    8    8   10   11   13   15   18   21   24   26   28   30   32   35   37 
LCS_GDT     S   148_A     S   148_A      5    6   16      3    4    5    6    7    8    9   10   12   13   15   16   17   19   21   24   27   30   32   35 
LCS_GDT     V   149_A     V   149_A      5    6   16      1    4    5    6    7    8    9   10   12   13   15   18   21   24   26   28   30   33   35   37 
LCS_GDT     H   150_A     H   150_A      7    7   16      4    6    6    7    7    8    9   10   11   13   14   15   17   18   20   25   27   30   33   36 
LCS_GDT     T   151_A     T   151_A      7    7   16      4    6    6    7    7    8   10   11   13   14   16   18   21   24   27   30   31   33   35   37 
LCS_GDT     T   152_A     T   152_A      7    7   16      4    6    6    7    7   10   11   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     N   153_A     N   153_A      7    7   16      4    6    6    7    7    8    9   10   12   14   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     P   154_A     P   154_A      7    7   16      3    6    6    7    7    8    9   10   12   14   16   19   21   25   27   30   31   33   35   37 
LCS_GDT     E   155_A     E   155_A      7    7   16      3    6    6    7    7    8    9   10   12   14   16   19   21   24   26   28   30   32   35   37 
LCS_GDT     L   156_A     L   156_A      7    7   16      3    4    5    7    7    8    9   10   12   14   16   19   21   24   26   28   30   32   35   37 
LCS_GDT     R   157_A     R   157_A      3    3   16      3    4    5    5    6    7    9    9   12   14   16   19   21   24   26   28   30   32   35   37 
LCS_GDT     V   158_A     V   158_A      3    3   17      3    4    5    5    6    7    9   10   12   14   16   19   21   23   26   27   29   32   34   37 
LCS_GDT     E   159_A     E   159_A      3    4   17      3    3    3    3    4    5    6   10   12   14   15   16   18   23   24   27   29   32   34   37 
LCS_GDT     L   160_A     L   160_A      5    8   17      3    4    5    6    8   10   11   11   13   13   14   15   16   19   20   24   27   30   34   37 
LCS_GDT     L   161_A     L   161_A      5    8   17      3    4    5    7    8   10   11   11   13   14   15   16   18   20   24   27   29   32   34   37 
LCS_GDT     N   162_A     N   162_A      6    8   17      3    4    6    7    8   10   11   11   13   14   15   16   18   20   22   27   29   32   34   37 
LCS_GDT     N   163_A     N   163_A      6    8   17      3    5    6    7    8   10   11   11   13   13   15   16   18   20   22   23   25   29   32   35 
LCS_GDT     R   164_A     R   164_A      6    8   17      4    5    6    7    8   10   11   11   13   13   14   15   15   16   20   22   23   26   31   32 
LCS_GDT     F   165_A     F   165_A      6    8   17      4    5    6    7    8   10   11   11   13   13   14   15   15   16   17   18   21   23   24   28 
LCS_GDT     A   166_A     A   166_A      6    8   17      4    5    6    7    7    7   11   11   13   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     G   167_A     G   167_A      6    8   17      4    5    6    7    7   10   11   11   13   13   14   15   15   16   17   18   20   23   24   27 
LCS_GDT     N   168_A     N   168_A      3    8   17      3    4    4    4    7   10   11   11   13   13   14   15   15   16   17   18   22   23   26   27 
LCS_GDT     I   169_A     I   169_A      4    5   17      3    4    4    6    8   10   11   11   13   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     Y   170_A     Y   170_A      4    5   17      3    4    4    6    8   10   11   11   13   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     E   171_A     E   171_A      4    4   17      3    4    4    4    5    6    8   10   13   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     R   172_A     R   172_A      4    4   17      3    4    4    4    6    6    9   11   13   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     M   173_A     M   173_A      3    4   17      3    4    4    4    5    7    7    8   10   13   14   15   15   16   17   18   21   23   24   27 
LCS_GDT     K   174_A     K   174_A      3    4   17      3    3    4    4    5    5    7    8    9   11   13   14   14   16   17   18   22   23   26   26 
LCS_GDT     K   175_A     K   175_A      3    4   17      3    3    4    4    5    5    7    8    9   11   14   16   18   18   21   21   23   24   26   30 
LCS_GDT     L   176_A     L   176_A      4    5   16      3    4    4    5    5    5    7    8    9   11   13   14   14   17   21   21   23   24   29   32 
LCS_GDT     A   177_A     A   177_A      4    5   16      3    4    4    5    5    5    6    8    9   11   14   16   18   18   21   21   23   24   26   27 
LCS_GDT     E   178_A     E   178_A      4    7   16      3    4    4    5    8   12   12   12   12   13   14   16   18   18   21   21   23   24   29   32 
LCS_GDT     G   179_A     G   179_A      4    7   16      3    4    4    5    8   12   12   12   12   13   14   16   18   18   21   23   25   30   32   34 
LCS_GDT     G   180_A     G   180_A      5    8   16      3    5    6    6    8   12   12   12   13   14   15   16   18   18   21   23   28   30   32   37 
LCS_GDT     I   181_A     I   181_A      5    8   16      3    6    7    8    8   12   12   13   15   15   16   17   18   20   23   26   31   33   34   37 
LCS_GDT     K   182_A     K   182_A      5    8   16      3    6    7    8    8   12   12   13   15   15   16   17   18   20   25   29   31   33   35   37 
LCS_GDT     M   183_A     M   183_A      5    8   16      3    6    7    8    8   12   12   13   15   15   16   18   22   25   27   30   31   33   35   37 
LCS_GDT     N   184_A     N   184_A      5    8   20      3    6    7    8    8   12   12   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     C   185_A     C   185_A      5    8   20      3    6    7    8    8   12   12   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     Q   186_A     Q   186_A      5    8   20      3    5    6    8    8   12   12   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     V   187_A     V   187_A      5    8   20      3    4    6    7    8   12   12   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     V   188_A     V   188_A      3    8   20      3    3    4    5    6    9   11   13   15   16   16   18   22   25   27   30   31   33   35   37 
LCS_GDT     L   189_A     L   189_A      4    4   20      3    4    4    5    5    7    8   11   13   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     C   190_A     C   190_A      4    4   20      3    4    4    5    5    7    8   11   13   13   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     P   191_A     P   191_A      4    5   20      3    4    5    5    6    7    8   11   13   14   16   19   21   25   27   30   31   33   35   37 
LCS_GDT     G   192_A     G   192_A      4    6   20      3    4    5    5    6    7    9   11   13   14   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     L   193_A     L   193_A      4    6   20      3    3    4    4    6    7   10   11   12   14   15   18   21   24   27   30   31   33   35   37 
LCS_GDT     N   194_A     N   194_A      4    6   20      3    5    5    6    8   12   12   12   12   13   14   16   19   23   25   28   30   33   35   37 
LCS_GDT     N   195_A     N   195_A      4    6   20      3    5    5    6    8   12   12   12   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     A   196_A     A   196_A      4    6   20      3    4    5    5    6    8    9   10   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     E   197_A     E   197_A      4    6   20      3    4    5    5    6    8    8   11   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     E   198_A     E   198_A      4    4   20      3    3    4    4    6    8    8   11   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     L   199_A     L   199_A      4    4   20      3    3    5    5    6    8    9   12   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     K   200_A     K   200_A      4    4   20      3    4    5    5    6    7    9   12   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     R   201_A     R   201_A      4    4   20      3    4    4    4    6    7    8   12   12   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     T   202_A     T   202_A      4    4   20      3    4    4    5    5    6    8    9   11   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     I   203_A     I   203_A      4    4   20      0    4    4    4    6   10   11   13   15   16   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     E   204_A     E   204_A      3    3   20      1    3    5    5    5   10   11   13   15   15   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     D   205_A     D   205_A      3    3   15      1    4    5    5    5   10   11   13   15   15   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     L   206_A     L   206_A      3    3   15      1    4    4    6    7    9   10   13   15   15   16   19   22   25   27   30   31   33   35   37 
LCS_GDT     Y   207_A     Y   207_A      3    3   13      0    6    7    8    8    9   10   12   15   15   16   17   20   25   27   30   31   33   35   37 
LCS_GDT     A   208_A     A   208_A      3    4   11      0    3    7    8    8    9   10   12   15   15   16   17   18   21   26   30   31   33   35   37 
LCS_GDT     L   209_A     L   209_A      3    4   11      3    3    5    5    6    7    8    9   13   14   15   17   18   21   26   30   31   33   35   37 
LCS_GDT     Y   210_A     Y   210_A      4    5   11      3    3    4    4    5    7    8    8   13   13   14   15   17   20   23   26   30   33   35   37 
LCS_GDT     P   211_A     P   211_A      4    5   11      3    3    4    4    5    7    8    8   13   13   14   15   17   20   23   26   30   33   35   37 
LCS_GDT     Q   212_A     Q   212_A      4    5   11      3    3    4    4    5    6    7    8    9   10   11   13   15   19   23   24   25   28   33   35 
LCS_GDT     V   213_A     V   213_A      4    5   11      3    3    4    4    5    6    7    8    9   10   12   13   15   19   23   24   25   27   29   35 
LCS_GDT     E   214_A     E   214_A      3    5   11      3    3    3    4    5    6    7    8    9   10   10   14   15   19   20   24   25   27   27   35 
LCS_AVERAGE  LCS_A:   2.04  (   1.01    1.31    3.81 )

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      4      6      7      8      8     12     12     13     15     16     16     19     22     25     27     30     31     33     35     37 
GDT PERCENT_AT   0.90   1.35   1.58   1.81   1.81   2.71   2.71   2.93   3.39   3.61   3.61   4.29   4.97   5.64   6.09   6.77   7.00   7.45   7.90   8.35
GDT RMS_LOCAL    0.20   0.60   0.77   1.14   1.14   2.16   2.16   2.62   3.12   3.79   3.34   4.32   4.96   5.24   5.55   6.02   6.16   6.50   6.63   7.02
GDT RMS_ALL_AT  25.62  25.57  19.54  19.16  19.16  17.11  17.11  18.59  18.54  21.19  18.46  18.79  19.04  18.95  18.93  18.40  18.03  18.60  17.68  16.36

# Checking swapping
#   possible swapping detected:  E   159_A      E   159_A
#   possible swapping detected:  E   198_A      E   198_A
#   possible swapping detected:  Y   207_A      Y   207_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N   146_A      N   146_A    18.185     0    0.567   1.204    19.324    0.000    0.000
LGA    I   147_A      I   147_A    15.763     0    0.090   1.115    16.341    0.000    0.000
LGA    S   148_A      S   148_A    16.367     0    0.228   0.717    19.723    0.000    0.000
LGA    V   149_A      V   149_A    10.834     0    0.584   0.597    12.707    0.000    2.041
LGA    H   150_A      H   150_A    11.364     0    0.632   1.196    18.130    0.119    0.048
LGA    T   151_A      T   151_A     6.082     0    0.061   1.170     9.115   30.119   19.116
LGA    T   152_A      T   152_A     2.730     0    0.187   0.234     5.597   43.214   41.497
LGA    N   153_A      N   153_A     8.266     0    0.145   1.002    13.569   10.238    5.179
LGA    P   154_A      P   154_A    10.341     0    0.128   0.151    13.032    0.000    0.000
LGA    E   155_A      E   155_A    14.772     0    0.623   1.006    19.047    0.000    0.000
LGA    L   156_A      L   156_A    15.942     0    0.630   1.367    16.212    0.000    0.000
LGA    R   157_A      R   157_A    16.246     0    0.626   1.143    17.970    0.000    0.000
LGA    V   158_A      V   158_A    20.396     0    0.614   1.471    22.702    0.000    0.000
LGA    E   159_A      E   159_A    26.387     0    0.638   0.911    30.623    0.000    0.000
LGA    L   160_A      L   160_A    26.463     0    0.128   0.885    28.199    0.000    0.000
LGA    L   161_A      L   161_A    27.475     0    0.371   0.770    29.891    0.000    0.000
LGA    N   162_A      N   162_A    31.520     0    0.076   0.941    32.246    0.000    0.000
LGA    N   163_A      N   163_A    33.029     0    0.292   1.263    34.970    0.000    0.000
LGA    R   164_A      R   164_A    36.558     0    0.225   0.925    39.907    0.000    0.000
LGA    F   165_A      F   165_A    37.074     0    0.147   1.193    38.932    0.000    0.000
LGA    A   166_A      A   166_A    35.395     0    0.179   0.184    35.968    0.000    0.000
LGA    G   167_A      G   167_A    36.479     0    0.250   0.250    36.479    0.000    0.000
LGA    N   168_A      N   168_A    32.991     0    0.699   0.529    33.792    0.000    0.000
LGA    I   169_A      I   169_A    31.075     0    0.603   1.320    33.391    0.000    0.000
LGA    Y   170_A      Y   170_A    27.699     0    0.641   1.310    29.323    0.000    0.000
LGA    E   171_A      E   171_A    28.896     0    0.362   0.439    29.239    0.000    0.000
LGA    R   172_A      R   172_A    30.175     0    0.339   0.990    40.167    0.000    0.000
LGA    M   173_A      M   173_A    26.270     0    0.646   0.660    27.980    0.000    0.000
LGA    K   174_A      K   174_A    26.442     0    0.617   1.195    34.005    0.000    0.000
LGA    K   175_A      K   175_A    21.960     0    0.592   0.773    23.887    0.000    0.000
LGA    L   176_A      L   176_A    18.671     0    0.582   0.669    20.535    0.000    0.000
LGA    A   177_A      A   177_A    18.839     0    0.656   0.636    21.187    0.000    0.000
LGA    E   178_A      E   178_A    16.874     0    0.555   1.159    20.317    0.000    0.000
LGA    G   179_A      G   179_A    11.756     0    0.060   0.060    13.279    1.310    1.310
LGA    G   180_A      G   180_A     7.170     0    0.627   0.627     9.138   12.500   12.500
LGA    I   181_A      I   181_A     3.540     0    0.090   1.023     4.861   45.476   48.333
LGA    K   182_A      K   182_A     1.622     0    0.065   1.319     4.416   75.119   64.603
LGA    M   183_A      M   183_A     1.376     0    0.173   0.518     2.764   77.381   76.369
LGA    N   184_A      N   184_A     1.944     0    0.124   0.940     4.207   72.857   67.440
LGA    C   185_A      C   185_A     2.480     0    0.120   0.163     3.495   57.262   58.492
LGA    Q   186_A      Q   186_A     2.364     0    0.105   1.195     8.165   77.381   48.201
LGA    V   187_A      V   187_A     1.161     0    0.048   1.007     4.670   73.214   60.884
LGA    V   188_A      V   188_A     3.289     0    0.278   1.102     6.894   39.405   51.429
LGA    L   189_A      L   189_A    10.419     0    0.596   1.113    14.067    1.786    0.893
LGA    C   190_A      C   190_A    13.847     0    0.263   0.350    14.909    0.000    0.000
LGA    P   191_A      P   191_A    16.109     0    0.531   0.611    17.890    0.000    0.000
LGA    G   192_A      G   192_A    18.382     0    0.232   0.232    18.382    0.000    0.000
LGA    L   193_A      L   193_A    17.071     0    0.102   1.465    21.236    0.000    0.000
LGA    N   194_A      N   194_A    17.512     0    0.325   1.226    18.265    0.000    0.000
LGA    N   195_A      N   195_A    15.367     0    0.515   1.468    18.396    0.000    0.000
LGA    A   196_A      A   196_A    14.790     0    0.335   0.487    15.102    0.000    0.000
LGA    E   197_A      E   197_A    16.758     0    0.112   1.205    21.810    0.000    0.000
LGA    E   198_A      E   198_A    12.490     0    0.620   1.000    16.830    0.000    0.000
LGA    L   199_A      L   199_A     8.001     0    0.120   1.469     9.467    5.119    8.810
LGA    K   200_A      K   200_A     7.883     0    0.621   0.680    12.032    5.476    3.968
LGA    R   201_A      R   201_A     9.442     0    0.092   1.064    15.258    2.381    0.866
LGA    T   202_A      T   202_A     6.438     0    0.625   0.619     8.161   18.452   14.694
LGA    I   203_A      I   203_A     2.557     0    0.604   0.934     3.652   51.905   55.655
LGA    E   204_A      E   204_A     2.591     0    0.629   0.540     4.729   52.619   54.339
LGA    D   205_A      D   205_A     2.658     0    0.638   0.851     8.699   67.024   40.714
LGA    L   206_A      L   206_A     4.092     0    0.618   1.396    10.738   44.048   24.405
LGA    Y   207_A      Y   207_A     6.471     0    0.659   1.483    10.330   20.476   10.794
LGA    A   208_A      A   208_A     6.530     0    0.691   0.623     7.000   16.310   15.048
LGA    L   209_A      L   209_A     7.767     0    0.669   1.433    10.545    3.690    2.262
LGA    Y   210_A      Y   210_A    13.156     0    0.037   1.171    20.230    0.000    0.000
LGA    P   211_A      P   211_A    15.075     0    0.703   0.576    17.046    0.000    0.000
LGA    Q   212_A      Q   212_A    16.530     0    0.317   0.572    18.263    0.000    0.000
LGA    V   213_A      V   213_A    16.960     0    0.590   1.381    18.653    0.000    0.000
LGA    E   214_A      E   214_A    19.780     0    0.171   1.161    23.973    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       69     276    276  100.00     550    550  100.00               443
SUMMARY(RMSD_GDC):    11.784         11.863                 12.227            2.043    1.783

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   69  443    4.0     13    2.62     3.217     2.632     0.478

LGA_LOCAL      RMSD:   2.620  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.586  Number of assigned atoms:   69 
Std_ASGN_ATOMS RMSD:  11.784  Standard rmsd on all 69 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.919011 * X  +   0.200628 * Y  +   0.339361 * Z  +  -0.165643
  Y_new =  -0.029968 * X  +  -0.893881 * Y  +   0.447302 * Z  +  26.384926
  Z_new =   0.393090 * X  +   0.400906 * Y  +   0.827499 * Z  +  -9.957063 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.108995 -0.403990  0.451154   [DEG: -178.1323  -23.1469   25.8492 ]
ZXZ:  2.492557  0.596158  0.775555   [DEG:  142.8130   34.1573   44.4360 ]
 
# END of job
