
#######################################################
#                                                     #
#                        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   57 (  461),  selected   57 , name one
# Molecule2: number of CA atoms  449 ( 3510),  selected   57 , 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:    18     171_A - 188_A       4.96    19.53
  LONGEST_CONTINUOUS_SEGMENT:    18     172_A - 189_A       4.49    20.40
  LCS_AVERAGE:      3.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11     150_A - 160_A       1.99    18.47
  LCS_AVERAGE:      1.72

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8     151_A - 158_A       0.93    19.69
  LONGEST_CONTINUOUS_SEGMENT:     8     152_A - 159_A       0.85    19.13
  LCS_AVERAGE:      1.12

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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   146_A     V   146_A      3    5   17      0    3    4    4   10   11   12   13   15   15   15   15   15   15   16   17   21   26   29   32 
LCS_GDT     F   147_A     F   147_A      4    5   17      3    3    4    4    5    6    8   13   15   15   15   15   15   17   17   19   22   26   29   32 
LCS_GDT     V   148_A     V   148_A      4    5   17      3    3    4    6    9   11   12   13   15   15   15   15   15   17   17   19   22   26   29   32 
LCS_GDT     H   149_A     H   149_A      4    5   17      3    3    4    4   10   11   12   13   15   15   15   15   16   17   18   19   22   28   29   32 
LCS_GDT     Q   150_A     Q   150_A      4   11   17      3    3    4    4    5    6   10   12   16   16   16   16   16   17   24   25   26   28   29   32 
LCS_GDT     S   151_A     S   151_A      8   11   17      5    7    8    9    9   11   12   14   16   16   16   16   16   17   21   23   25   28   28   30 
LCS_GDT     G   152_A     G   152_A      8   11   17      5    7    8    9   10   11   12   14   16   16   16   17   19   22   24   25   26   28   29   32 
LCS_GDT     C   153_A     C   153_A      8   11   17      5    7    8    9   10   11   12   13   15   15   16   20   21   22   24   25   26   28   29   32 
LCS_GDT     Y   154_A     Y   154_A      8   11   17      5    7    8    9   10   11   12   13   15   15   15   16   17   18   21   25   26   28   29   32 
LCS_GDT     V   155_A     V   155_A      8   11   17      5    7    8    9   10   11   12   13   15   15   15   16   17   17   19   24   24   27   29   32 
LCS_GDT     K   156_A     K   156_A      8   11   17      4    7    8    9   10   11   12   13   15   15   15   16   17   17   18   19   21   26   29   32 
LCS_GDT     P   157_A     P   157_A      8   11   17      4    7    8    9   10   11   12   13   15   15   15   15   17   17   18   18   19   23   24   26 
LCS_GDT     E   158_A     E   158_A      8   11   17      3    6    8    9   10   11   12   13   15   15   15   16   17   17   18   19   20   24   24   29 
LCS_GDT     E   159_A     E   159_A      8   11   17      3    6    8    9   10   11   12   13   15   15   15   16   17   17   18   19   23   26   29   32 
LCS_GDT     P   160_A     P   160_A      5   11   17      3    3    5    8    9   10   10   12   15   15   15   16   17   17   18   19   22   26   29   32 
LCS_GDT     P   161_A     P   161_A      3    3   17      3    3    3    3    4    5    6    8    9   11   13   16   17   17   18   19   23   26   29   32 
LCS_GDT     F   162_A     F   162_A      3    5   17      0    3    3    4    5    9   13   16   17   19   20   21   21   22   23   25   26   27   29   32 
LCS_GDT     Y   163_A     Y   163_A      3    5   13      5    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     A   164_A     A   164_A      3    5   13      3    3    5    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     P   165_A     P   165_A      3    5   13      3    3    3    5   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     C   166_A     C   166_A      3    5   13      3    3    6    8   10   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     L   167_A     L   167_A      3    4   12      4    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     A   168_A     A   168_A      3    5   12      3    3    4    5    8   10   12   15   17   18   20   21   21   22   24   25   26   28   29   31 
LCS_GDT     Q   169_A     Q   169_A      4    5   12      3    4    4    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     S   170_A     S   170_A      4    6   12      3    4    4    4    5    7    9   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     W   171_A     W   171_A      5    6   18      3    5    5    5    5    7    8    8   10   13   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     S   172_A     S   172_A      5    6   18      4    5    5    5    5    7    8    8    9    9   14   17   17   18   18   24   25   27   29   30 
LCS_GDT     Q   173_A     Q   173_A      5    6   18      4    5    5    5    5    7   10   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     E   174_A     E   174_A      5    9   18      4    5    6    6    7    9   10   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     D   175_A     D   175_A      5    9   18      4    5    6    6    7    9   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     K   176_A     K   176_A      5    9   18      3    5    5    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     T   177_A     T   177_A      5    9   18      4    5    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     F   178_A     F   178_A      5    9   18      4    5    6    6    8   10   11   11   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     T   179_A     T   179_A      6    9   18      4    6    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     M   180_A     M   180_A      6    9   18      4    6    6    6    8   10   11   11   13   14   16   16   17   18   18   18   19   22   23   25 
LCS_GDT     L   181_A     L   181_A      6    9   18      4    6    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     S   182_A     S   182_A      6    9   18      3    6    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     W   183_A     W   183_A      6    9   18      4    6    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     G   184_A     G   184_A      6    9   18      4    6    6    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     I   185_A     I   185_A      4    9   18      3    3    4    6    8   10   11   12   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     V   186_A     V   186_A      4    6   18      3    4    4    4    5    6    9   12   13   15   16   17   17   18   18   18   20   22   25   28 
LCS_GDT     P   187_A     P   187_A      4    6   18      3    4    4    4    5    6    7   10   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     Q   188_A     Q   188_A      4    6   18      3    4    4    5    5    6    7   10   14   15   16   17   17   18   18   18   20   22   23   25 
LCS_GDT     V   189_A     V   189_A      4    6   18      3    4    4    5    5    6    7    9   10   13   16   17   17   18   18   19   20   22   26   27 
LCS_GDT     T   190_A     T   190_A      4    6   15      3    4    4    5    6    8   11   14   16   16   16   16   19   21   24   25   26   28   29   31 
LCS_GDT     S   191_A     S   191_A      4    7   15      3    4    4    5    6    8   11   14   16   16   19   20   21   22   24   25   26   28   29   32 
LCS_GDT     T   192_A     T   192_A      4    8   15      5    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     L   193_A     L   193_A      5    8   15      5    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     V   194_A     V   194_A      5    8   15      5    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     S   195_A     S   195_A      5    8   15      4    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     E   196_A     E   196_A      5    8   15      3    5    6    7   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     V   197_A     V   197_A      5    8   15      3    5    6    7    8   11   12   15   17   19   20   21   21   22   24   25   26   28   29   31 
LCS_GDT     L   198_A     L   198_A      5    8   15      4    5    6    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     Y   199_A     Y   199_A      5    8   15      4    5    5    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     Y   200_A     Y   200_A      5    8   15      5    6    7    9   12   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     T   201_A     T   201_A      5    8   15      4    5    5    7   11   14   15   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_GDT     R   202_A     R   202_A      5    7   15      4    4    5    6    8    9   13   17   17   19   20   21   21   22   24   25   26   28   29   32 
LCS_AVERAGE  LCS_A:   2.15  (   1.12    1.72    3.62 )

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      7      8      9     12     14     15     17     17     19     20     21     21     22     24     25     26     28     29     32 
GDT PERCENT_AT   1.11   1.56   1.78   2.00   2.67   3.12   3.34   3.79   3.79   4.23   4.45   4.68   4.68   4.90   5.35   5.57   5.79   6.24   6.46   7.13
GDT RMS_LOCAL    0.36   0.57   0.85   1.01   1.72   1.95   2.15   2.74   2.74   3.04   3.24   3.54   3.58   3.85   4.86   5.09   5.31   5.75   6.05   7.28
GDT RMS_ALL_AT  20.26  19.86  19.13  19.52  14.82  14.96  14.62  14.11  14.11  14.26  14.21  14.07  14.03  13.88  13.09  13.03  13.04  13.05  12.85  13.33

# Checking swapping
#   possible swapping detected:  Y   154_A      Y   154_A
#   possible swapping detected:  E   158_A      E   158_A
#   possible swapping detected:  E   159_A      E   159_A
#   possible swapping detected:  F   162_A      F   162_A
#   possible swapping detected:  Y   163_A      Y   163_A
#   possible swapping detected:  D   175_A      D   175_A
#   possible swapping detected:  F   178_A      F   178_A
#   possible swapping detected:  Y   200_A      Y   200_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V   146_A      V   146_A    16.695     0    0.653   0.661    20.009    0.000    0.000
LGA    F   147_A      F   147_A    16.418     0    0.668   1.164    18.391    0.000    0.000
LGA    V   148_A      V   148_A    15.514     0    0.140   1.159    16.468    0.000    0.000
LGA    H   149_A      H   149_A    15.732     0    0.558   1.126    21.855    0.000    0.000
LGA    Q   150_A      Q   150_A    13.059     0    0.082   0.754    14.038    0.000    0.053
LGA    S   151_A      S   151_A    16.297     0    0.556   0.702    18.152    0.000    0.000
LGA    G   152_A      G   152_A    13.666     0    0.127   0.127    14.356    0.000    0.000
LGA    C   153_A      C   153_A    12.080     0    0.069   0.713    13.258    0.000    0.000
LGA    Y   154_A      Y   154_A    14.416     0    0.038   1.322    15.154    0.000    0.000
LGA    V   155_A      V   155_A    15.360     0    0.033   0.140    18.082    0.000    0.000
LGA    K   156_A      K   156_A    19.502     0    0.085   0.716    24.168    0.000    0.000
LGA    P   157_A      P   157_A    21.563     0    0.124   0.185    24.744    0.000    0.000
LGA    E   158_A      E   158_A    19.686     0    0.214   1.124    22.570    0.000    0.000
LGA    E   159_A      E   159_A    15.370     0    0.584   1.050    16.916    0.000    0.000
LGA    P   160_A      P   160_A    14.931     0    0.603   0.809    18.255    0.000    0.000
LGA    P   161_A      P   161_A    10.999     0    0.638   0.661    13.267    1.905    1.088
LGA    F   162_A      F   162_A     5.278     0    0.575   0.520     7.931   30.833   20.000
LGA    Y   163_A      Y   163_A     1.228     0    0.618   1.229     7.179   77.262   43.770
LGA    A   164_A      A   164_A     2.293     0    0.156   0.176     2.816   70.833   68.095
LGA    P   165_A      P   165_A     2.440     0    0.659   0.605     4.259   57.857   50.748
LGA    C   166_A      C   166_A     3.016     0    0.613   0.896     7.632   71.548   52.460
LGA    L   167_A      L   167_A     2.644     0    0.195   0.979     6.245   48.214   51.488
LGA    A   168_A      A   168_A     5.939     0    0.650   0.604     8.504   33.214   27.143
LGA    Q   169_A      Q   169_A     2.793     0    0.639   1.232     3.712   55.595   58.148
LGA    S   170_A      S   170_A     4.651     0    0.130   0.552     8.430   33.095   26.429
LGA    W   171_A      W   171_A     7.494     0    0.592   1.222    14.163    6.905    2.619
LGA    S   172_A      S   172_A    12.936     0    0.091   0.192    15.549    0.000    0.000
LGA    Q   173_A      Q   173_A    19.386     0    0.063   1.049    25.220    0.000    0.000
LGA    E   174_A      E   174_A    23.372     0    0.153   0.795    26.195    0.000    0.000
LGA    D   175_A      D   175_A    20.591     0    0.518   1.288    20.978    0.000    0.000
LGA    K   176_A      K   176_A    22.813     0    0.513   1.025    31.881    0.000    0.000
LGA    T   177_A      T   177_A    22.372     0    0.122   0.899    24.583    0.000    0.000
LGA    F   178_A      F   178_A    22.453     0    0.119   1.236    23.409    0.000    0.000
LGA    T   179_A      T   179_A    22.003     0    0.144   1.068    24.483    0.000    0.000
LGA    M   180_A      M   180_A    21.997     0    0.182   0.921    22.891    0.000    0.000
LGA    L   181_A      L   181_A    19.647     0    0.038   0.315    20.818    0.000    0.000
LGA    S   182_A      S   182_A    19.715     0    0.134   0.597    21.305    0.000    0.000
LGA    W   183_A      W   183_A    18.679     0    0.062   1.225    19.322    0.000    0.000
LGA    G   184_A      G   184_A    18.677     0    0.664   0.664    19.702    0.000    0.000
LGA    I   185_A      I   185_A    17.521     0    0.637   1.416    17.729    0.000    0.000
LGA    V   186_A      V   186_A    14.415     0    0.416   0.929    15.227    0.000    0.000
LGA    P   187_A      P   187_A    15.319     0    0.129   0.158    16.478    0.000    0.000
LGA    Q   188_A      Q   188_A    16.044     0    0.667   1.001    18.271    0.000    0.000
LGA    V   189_A      V   189_A    18.034     0    0.186   1.199    21.050    0.000    0.000
LGA    T   190_A      T   190_A    12.261     0    0.051   1.273    14.013    0.357    0.204
LGA    S   191_A      S   191_A     7.662     0    0.076   0.522    10.229   14.048    9.603
LGA    T   192_A      T   192_A     1.086     0    0.669   0.526     4.894   73.571   59.864
LGA    L   193_A      L   193_A     1.378     0    0.103   0.997     2.118   81.429   77.202
LGA    V   194_A      V   194_A     1.605     0    0.130   0.216     3.258   79.405   72.177
LGA    S   195_A      S   195_A     0.772     0    0.129   0.454     3.450   83.810   75.000
LGA    E   196_A      E   196_A     3.391     0    0.458   0.795     7.261   44.524   32.434
LGA    V   197_A      V   197_A     5.085     0    0.039   0.232     8.162   40.952   27.891
LGA    L   198_A      L   198_A     3.018     0    0.045   0.564     6.564   42.143   36.726
LGA    Y   199_A      Y   199_A     2.755     0    0.084   1.081    13.279   65.000   28.333
LGA    Y   200_A      Y   200_A     2.121     0    0.048   0.420     7.484   72.976   39.325
LGA    T   201_A      T   201_A     2.282     0    0.567   0.751     5.086   61.190   51.088
LGA    R   202_A      R   202_A     5.011     0    0.105   1.108     7.267   30.595   22.857

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     461    461  100.00               449
SUMMARY(RMSD_GDC):    11.652         11.647                 12.054            2.622    2.082

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  449    4.0     17    2.74     3.229     2.937     0.599

LGA_LOCAL      RMSD:   2.739  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.114  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  11.652  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.802790 * X  +   0.269490 * Y  +   0.531887 * Z  + -37.615047
  Y_new =  -0.087157 * X  +  -0.829418 * Y  +   0.551788 * Z  + -14.012782
  Z_new =   0.589858 * X  +  -0.489327 * Y  +  -0.642360 * Z  +  24.236574 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.108144 -0.630883 -2.490605   [DEG:   -6.1962  -36.1469 -142.7012 ]
ZXZ:  2.374557  2.268371  2.263308   [DEG:  136.0521  129.9681  129.6780 ]
 
# END of job
