
#######################################################
#                                                     #
#                        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   61 (  435),  selected   61 , name one
# Molecule2: number of CA atoms  325 ( 2539),  selected   61 , 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:    21     165_A - 185_A       4.74    17.99
  LCS_AVERAGE:      5.47

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12     166_A - 177_A       1.86    15.04
  LONGEST_CONTINUOUS_SEGMENT:    12     167_A - 178_A       1.99    15.16
  LCS_AVERAGE:      2.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8     167_A - 174_A       0.99    18.30
  LCS_AVERAGE:      1.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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      3    3   13      0    3    3    3    8    8    8    8    8   10   10   11   12   13   14   16   19   22   24   25 
LCS_GDT     A   147_A     A   147_A      3    3   13      3    3    3    3    4    5    6    8    8   10   10   11   12   13   15   17   19   22   24   25 
LCS_GDT     S   148_A     S   148_A      6    6   13      5    5    6    6    6    6    7    9    9   10   10   11   13   15   17   18   20   22   24   25 
LCS_GDT     A   149_A     A   149_A      6    6   13      5    5    6    6    6    6    7    9    9   10   10   11   14   16   17   18   20   21   24   25 
LCS_GDT     L   150_A     L   150_A      6    6   13      5    5    6    6    6    6    7    9    9    9    9   11   13   14   15   16   18   21   22   23 
LCS_GDT     L   151_A     L   151_A      6    6   13      5    5    6    6    6    6    7    9    9   10   10   11   13   14   15   17   19   22   24   25 
LCS_GDT     A   152_A     A   152_A      6    6   13      5    5    6    6    6    6    7    9    9   10   10   11   13   16   17   18   20   22   24   25 
LCS_GDT     G   153_A     G   153_A      6    6   15      1    4    6    6    6    6    7    9    9   10   10   11   13   16   17   18   20   22   24   25 
LCS_GDT     L   154_A     L   154_A      3    4   16      0    4    4    4    4    5    7    9    9   10   11   13   14   16   17   18   20   22   24   25 
LCS_GDT     G   155_A     G   155_A      3    4   16      0    4    4    4    4    5    7    9   10   10   13   13   14   16   17   18   20   22   24   25 
LCS_GDT     A   156_A     A   156_A      3    3   16      0    3    3    3    3    4    6    9   10   11   13   13   14   16   17   18   20   22   24   25 
LCS_GDT     R   157_A     R   157_A      3    3   16      3    3    3    3    3    5    7    9   10   11   13   13   14   16   17   18   20   22   24   29 
LCS_GDT     L   158_A     L   158_A      4    4   16      3    3    5    5    6    6    8    9   10   11   13   15   17   18   22   23   27   29   29   29 
LCS_GDT     A   159_A     A   159_A      4    4   16      3    3    5    5    5    6    8    9   10   11   14   16   17   18   20   22   27   29   29   29 
LCS_GDT     A   160_A     A   160_A      4    4   17      3    3    5    5    5    6    7    9   10   11   14   16   17   18   20   22   27   29   29   29 
LCS_GDT     L   161_A     L   161_A      4    6   19      3    4    5    5    6    6    8    9   10   12   14   16   17   20   22   23   27   29   29   29 
LCS_GDT     R   162_A     R   162_A      4    6   19      3    4    4    5    6    6    7    9   11   12   14   16   17   20   22   23   27   29   29   29 
LCS_GDT     T   163_A     T   163_A      4    6   19      3    4    4    5    6    6    8    9   11   11   14   16   18   20   22   23   27   29   29   29 
LCS_GDT     S   164_A     S   164_A      4    6   19      3    4    5    5    6    6    8    9   11   12   14   16   18   20   22   23   27   29   29   29 
LCS_GDT     G   165_A     G   165_A      4    7   21      3    3    4    5    7    8   10   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     T   166_A     T   166_A      4   12   21      3    3    5    9   11   12   13   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     F   167_A     F   167_A      8   12   21      5    6    8    9   11   12   13   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     S   168_A     S   168_A      8   12   21      5    6    8    9   11   12   13   13   14   16   18   19   19   19   20   23   27   29   29   29 
LCS_GDT     P   169_A     P   169_A      8   12   21      5    6    8    9   11   12   13   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     L   170_A     L   170_A      8   12   21      5    6    8    9   11   12   13   13   14   16   18   19   19   19   20   23   27   29   29   29 
LCS_GDT     P   171_A     P   171_A      8   12   21      5    6    8    9   11   12   13   13   14   16   18   19   19   19   20   22   27   29   29   29 
LCS_GDT     T   172_A     T   172_A      8   12   21      3    6    8    9   11   12   13   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     E   173_A     E   173_A      8   12   21      4    6    8    9   11   12   13   13   14   16   18   19   19   19   20   23   27   29   29   29 
LCS_GDT     A   174_A     A   174_A      8   12   21      3    5    8    8   10   11   13   13   14   16   18   19   19   20   22   23   27   29   29   29 
LCS_GDT     V   175_A     V   175_A      6   12   21      4    6    7    9   11   12   13   13   14   16   18   20   22   22   24   25   27   29   29   30 
LCS_GDT     S   176_A     S   176_A      6   12   21      3    5    6    9   11   12   13   13   14   16   18   20   22   22   24   25   27   29   29   30 
LCS_GDT     E   177_A     E   177_A      6   12   21      3    5    7    9   11   12   13   13   14   16   18   20   22   22   24   25   27   29   29   30 
LCS_GDT     A   178_A     A   178_A      6   12   21      3    4    6    7   10   12   13   13   14   16   18   20   22   22   24   25   27   29   29   30 
LCS_GDT     G   179_A     G   179_A      5    5   21      3    4    5    5    5    6    9   11   13   16   17   20   22   22   24   25   27   29   29   30 
LCS_GDT     G   180_A     G   180_A      5    5   21      3    4    5    5    6    6    8   12   14   16   18   20   22   22   24   25   27   29   29   30 
LCS_GDT     D   181_A     D   181_A      5    5   21      3    4    5    5    5    5    6    7    9   11   12   15   18   20   22   23   27   29   29   30 
LCS_GDT     V   182_A     V   182_A      5    5   21      3    4    5    5    5    5    5    7    9   11   12   15   18   20   22   23   27   29   29   30 
LCS_GDT     A   183_A     A   183_A      4    5   21      3    4    4    4    5    5    9   12   14   16   18   19   19   20   22   23   27   29   29   30 
LCS_GDT     R   184_A     R   184_A      4    5   21      3    4    4    4    5    7    9   12   14   16   18   19   19   20   22   23   27   29   29   30 
LCS_GDT     L   185_A     L   185_A      3    5   21      3    3    4    4    5    5    6   10   14   16   18   19   19   20   22   25   27   29   29   30 
LCS_GDT     L   186_A     L   186_A      3    4   20      3    3    3    4    4    5    9    9   11   12   14   18   22   22   24   25   27   29   29   30 
LCS_GDT     L   187_A     L   187_A      4    4   17      3    3    5    5    6    6    9   10   11   12   12   16   22   22   24   25   26   28   29   30 
LCS_GDT     S   188_A     S   188_A      4    4   17      3    3    5    5    6    6    9   10   11   12   14   20   22   22   24   25   26   28   29   30 
LCS_GDT     P   189_A     P   189_A      4    4   17      3    3    5    5    6    7    9   10   11   12   12   14   17   21   24   25   26   28   29   30 
LCS_GDT     S   190_A     S   190_A      4    4   17      3    3    4    5    6    7    9   10   11   12   12   20   22   22   24   25   26   28   29   30 
LCS_GDT     V   191_A     V   191_A      3    6   17      3    4    4    5    5    7    9   10   11   12   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     Q   192_A     Q   192_A      3    6   17      3    3    4    5    5    6    7    7    8    9   11   12   15   16   23   24   26   28   29   30 
LCS_GDT     R   193_A     R   193_A      3    6   17      3    4    5    5    6    6    7    8    9   10   11   14   16   20   24   25   26   28   29   30 
LCS_GDT     D   194_A     D   194_A      3    6   17      3    4    4    5    5    6    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     V   195_A     V   195_A      4    6   17      3    4    5    5    6    9   12   13   14   14   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     L   196_A     L   196_A      4    6   17      3    4    5    5    6    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     P   197_A     P   197_A      4    5   17      3    4    5    5    6    7    9   10   11   12   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     G   198_A     G   198_A      4    7   17      3    4    5    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     G   199_A     G   199_A      6    7   17      3    5    6    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     T   200_A     T   200_A      6    7   17      3    5    6    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     I   201_A     I   201_A      6    7   17      4    5    6    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     I   202_A     I   202_A      6    7   17      4    5    6    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     Q   203_A     Q   203_A      6    7   17      4    5    6    6    8    8    9   10   11   13   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     D   204_A     D   204_A      6    7   13      4    5    6    6    8    8    9   10   10   12   17   20   22   22   24   25   26   28   29   30 
LCS_GDT     W   205_A     W   205_A      3    3   13      3    3    3    3    3    5    8    8    8    8   10   11   13   16   20   21   25   26   27   30 
LCS_GDT     Q   206_A     Q   206_A      3    3   13      0    3    3    3    3    3    5    5    8    8    9    9   10   13   14   16   17   20   27   30 
LCS_AVERAGE  LCS_A:   3.01  (   1.50    2.05    5.47 )

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      5      6      8      9     11     12     13     13     14     16     18     20     22     22     24     25     27     29     29     30 
GDT PERCENT_AT   1.54   1.85   2.46   2.77   3.38   3.69   4.00   4.00   4.31   4.92   5.54   6.15   6.77   6.77   7.38   7.69   8.31   8.92   8.92   9.23
GDT RMS_LOCAL    0.19   0.62   0.99   1.38   1.60   1.83   2.05   2.05   2.38   3.74   4.02   4.50   4.90   4.90   5.33   5.59   6.21   6.68   6.46   6.70
GDT RMS_ALL_AT  36.00  17.22  18.30  14.93  15.09  15.33  15.24  15.24  15.82  19.08  17.99  19.56  19.73  19.73  19.87  19.93  18.43  18.09  20.42  20.49

# Checking swapping
#   possible swapping detected:  F   167_A      F   167_A
#   possible swapping detected:  D   204_A      D   204_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N   146_A      N   146_A    27.016     0    0.159   1.171    29.948    0.000    0.000
LGA    A   147_A      A   147_A    22.809     0    0.590   0.591    24.945    0.000    0.000
LGA    S   148_A      S   148_A    25.935     0    0.617   0.591    26.968    0.000    0.000
LGA    A   149_A      A   149_A    28.342     0    0.037   0.047    30.293    0.000    0.000
LGA    L   150_A      L   150_A    27.195     0    0.031   1.399    30.022    0.000    0.000
LGA    L   151_A      L   151_A    22.236     0    0.033   0.281    24.109    0.000    0.000
LGA    A   152_A      A   152_A    22.811     0    0.684   0.633    25.022    0.000    0.000
LGA    G   153_A      G   153_A    22.861     0    0.712   0.712    22.861    0.000    0.000
LGA    L   154_A      L   154_A    18.208     0    0.635   1.177    19.803    0.000    0.000
LGA    G   155_A      G   155_A    16.699     0    0.597   0.597    17.441    0.000    0.000
LGA    A   156_A      A   156_A    19.553     0    0.627   0.607    22.076    0.000    0.000
LGA    R   157_A      R   157_A    15.215     0    0.603   0.965    16.423    0.000    0.000
LGA    L   158_A      L   158_A    12.166     0    0.626   1.285    13.157    0.000    0.000
LGA    A   159_A      A   159_A    12.153     0    0.039   0.040    13.333    0.000    0.000
LGA    A   160_A      A   160_A    13.816     0    0.591   0.582    15.253    0.000    0.000
LGA    L   161_A      L   161_A    12.937     0    0.628   0.756    14.327    0.000    0.000
LGA    R   162_A      R   162_A    16.294     0    0.582   1.135    22.715    0.000    0.000
LGA    T   163_A      T   163_A    18.288     0    0.411   1.342    21.852    0.000    0.000
LGA    S   164_A      S   164_A    12.882     0    0.711   0.655    15.114    0.000    0.000
LGA    G   165_A      G   165_A     6.773     0    0.735   0.735     8.827   19.762   19.762
LGA    T   166_A      T   166_A     2.363     0    0.595   1.437     3.807   67.857   71.224
LGA    F   167_A      F   167_A     1.355     0    0.129   1.491     8.921   79.524   39.567
LGA    S   168_A      S   168_A     1.202     0    0.163   0.263     2.171   81.429   77.222
LGA    P   169_A      P   169_A     0.907     0    0.113   0.318     1.337   90.476   89.184
LGA    L   170_A      L   170_A     1.310     0    0.124   0.211     1.911   81.429   79.286
LGA    P   171_A      P   171_A     2.014     0    0.057   0.167     4.221   79.643   64.150
LGA    T   172_A      T   172_A     0.815     0    0.162   1.077     3.394   81.548   71.293
LGA    E   173_A      E   173_A     1.828     0    0.091   0.996     3.965   61.548   62.751
LGA    A   174_A      A   174_A     3.586     0    0.084   0.082     5.165   65.952   58.000
LGA    V   175_A      V   175_A     2.092     0    0.129   1.051     5.537   64.881   54.490
LGA    S   176_A      S   176_A     1.734     0    0.095   0.514     3.771   67.262   60.397
LGA    E   177_A      E   177_A     2.378     0    0.569   1.428     4.496   59.881   50.794
LGA    A   178_A      A   178_A     3.080     0    0.652   0.622     5.100   47.262   49.238
LGA    G   179_A      G   179_A     9.036     0    0.732   0.732    10.986    3.810    3.810
LGA    G   180_A      G   180_A    10.257     0    0.246   0.246    13.493    0.357    0.357
LGA    D   181_A      D   181_A    15.052     0    0.628   0.571    18.955    0.000    0.000
LGA    V   182_A      V   182_A    14.951     0    0.610   0.623    16.039    0.000    0.000
LGA    A   183_A      A   183_A    16.865     0    0.409   0.412    18.414    0.000    0.000
LGA    R   184_A      R   184_A    16.646     0    0.667   1.327    19.269    0.000    0.000
LGA    L   185_A      L   185_A    14.014     0    0.588   0.831    16.362    0.000    0.000
LGA    L   186_A      L   186_A    10.598     0    0.670   0.895    13.363    0.000   10.060
LGA    L   187_A      L   187_A    13.578     0    0.623   0.908    17.739    0.000    0.000
LGA    S   188_A      S   188_A    11.242     0    0.141   0.152    12.463    0.000    0.714
LGA    P   189_A      P   189_A    15.603     0    0.657   0.874    17.548    0.000    0.000
LGA    S   190_A      S   190_A    12.716     0    0.650   0.708    14.004    0.000    0.079
LGA    V   191_A      V   191_A    12.311     0    0.614   0.630    13.492    0.000    0.000
LGA    Q   192_A      Q   192_A    17.108     0    0.559   1.257    23.911    0.000    0.000
LGA    R   193_A      R   193_A    15.594     0    0.473   1.192    20.862    0.000    0.000
LGA    D   194_A      D   194_A    10.792     0    0.693   0.733    12.241    0.714    0.476
LGA    V   195_A      V   195_A     7.036     0    0.575   0.569    10.412    4.405   11.905
LGA    L   196_A      L   196_A    11.039     0    0.057   0.933    13.366    0.357    0.179
LGA    P   197_A      P   197_A    13.482     0    0.186   0.538    15.891    0.000    0.000
LGA    G   198_A      G   198_A    15.802     0    0.564   0.564    20.022    0.000    0.000
LGA    G   199_A      G   199_A    19.553     0    0.700   0.700    19.660    0.000    0.000
LGA    T   200_A      T   200_A    20.219     0    0.031   1.112    24.207    0.000    0.000
LGA    I   201_A      I   201_A    17.221     0    0.135   1.122    18.352    0.000    0.000
LGA    I   202_A      I   202_A    17.400     0    0.073   0.150    22.147    0.000    0.000
LGA    Q   203_A      Q   203_A    14.214     0    0.082   1.600    15.917    0.000    0.000
LGA    D   204_A      D   204_A    16.763     0    0.405   1.497    19.697    0.000    0.000
LGA    W   205_A      W   205_A    19.839     0    0.677   1.213    23.131    0.000    0.000
LGA    Q   206_A      Q   206_A    23.001     0    0.059   0.817    25.745    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     435    435  100.00               325
SUMMARY(RMSD_GDC):    14.478         14.417                 14.893            2.948    2.692

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61  325    4.0     13    2.05     4.077     3.691     0.604

LGA_LOCAL      RMSD:   2.054  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.243  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:  14.478  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.402377 * X  +   0.535277 * Y  +   0.742678 * Z  +   7.892516
  Y_new =  -0.194157 * X  +  -0.742898 * Y  +   0.640629 * Z  +  68.931129
  Z_new =   0.894648 * X  +  -0.401970 * Y  +  -0.194998 * Z  +   9.236950 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.449569 -1.107644 -2.022457   [DEG:  -25.7584  -63.4633 -115.8782 ]
ZXZ:  2.282556  1.767051  1.993072   [DEG:  130.7808  101.2446  114.1946 ]
 
# END of job
