
#######################################################
#                                                     #
#                        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   37 (  280),  selected   37 , name one
# Molecule2: number of CA atoms  141 ( 1131),  selected   37 , 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:    24     112_A - 135_A       4.52    11.88
  LCS_AVERAGE:     14.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     116_A - 135_A       1.91    14.42
  LCS_AVERAGE:      9.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17     119_A - 135_A       0.71    14.28
  LCS_AVERAGE:      7.09

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     T    99_A     T    99_A      3    3   11      0    3    3    3    3    4    5    8    9   17   18   20   21   23   25   27   28   28   30   31 
LCS_GDT     N   100_A     N   100_A      4    4   14      3    3    4    5    6    8    9   11   15   16   17   20   21   23   25   27   28   28   30   31 
LCS_GDT     A   101_A     A   101_A      4    4   16      3    3    4    5    6   10   12   14   15   16   18   20   21   23   25   27   28   28   30   31 
LCS_GDT     Y   102_A     Y   102_A      4    4   16      3    3    4    5    5    6    8    9   10   15   17   19   21   23   25   27   28   28   30   31 
LCS_GDT     I   103_A     I   103_A      4    4   16      2    3    4    5    5    6    8    9   10   11   14   16   19   22   24   26   27   28   30   31 
LCS_GDT     A   104_A     A   104_A      4    6   16      4    4    4    5    5    6    8    9   10   11   12   16   17   22   24   26   27   28   30   31 
LCS_GDT     V   105_A     V   105_A      4    6   16      4    4    4    5    5    6    8    8    9    9   10   13   14   17   17   18   25   28   30   31 
LCS_GDT     L   106_A     L   106_A      4    6   16      4    4    4    5    5    6    8    8    9    9    9   10   13   14   15   16   17   19   20   21 
LCS_GDT     E   107_A     E   107_A      4    6   16      4    4    4    5    5    6    8    9   10   11   12   14   15   16   18   20   22   23   27   29 
LCS_GDT     G   108_A     G   108_A      3    6   16      3    3    4    5    5    6    8    9   10   11   14   16   17   22   24   26   26   28   30   31 
LCS_GDT     D   109_A     D   109_A      3    6   16      3    3    3    4    5    6    8    9   10   11   14   16   17   22   22   26   26   28   30   31 
LCS_GDT     P   110_A     P   110_A      3    4   16      3    3    3    4    4    5    7    9    9   11   14   16   17   22   24   26   26   28   30   31 
LCS_GDT     E   111_A     E   111_A      3    4   16      3    3    3    5    5    6    8    9   10   11   14   16   18   22   24   26   27   28   30   31 
LCS_GDT     A   112_A     A   112_A      3    3   24      3    3    3    5    5    6    8   10   13   15   17   19   21   23   25   27   28   28   30   31 
LCS_GDT     I   113_A     I   113_A      5    5   24      3    4    5    5    5    6    7   13   15   16   18   21   21   23   25   27   28   28   30   31 
LCS_GDT     A   114_A     A   114_A      5    5   24      3    4    5    5    5    6    7    8   10   11   12   15   18   23   25   27   28   28   30   31 
LCS_GDT     R   115_A     R   115_A      5    5   24      3    4    5    5    5    6    7    8   10   12   15   19   21   23   25   27   28   28   30   31 
LCS_GDT     F   116_A     F   116_A      5   20   24      3    4    5   11   14   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     L   117_A     L   117_A      5   20   24      0    3    8   11   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     G   118_A     G   118_A      6   20   24      3    4    6    7   11   13   18   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     I   119_A     I   119_A     17   20   24      5   10   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     S   120_A     S   120_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     L   121_A     L   121_A     17   20   24     10   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   29   29 
LCS_GDT     E   122_A     E   122_A     17   20   24     10   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   29   31 
LCS_GDT     E   123_A     E   123_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     V   124_A     V   124_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     Q   125_A     Q   125_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     E   126_A     E   126_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     I   127_A     I   127_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     I   128_A     I   128_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     D   129_A     D   129_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     A   130_A     A   130_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     A   131_A     A   131_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     R   132_A     R   132_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     K   133_A     K   133_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     A   134_A     A   134_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_GDT     V   135_A     V   135_A     17   20   24     13   16   17   17   17   18   19   20   20   20   20   21   21   23   25   27   28   28   30   31 
LCS_AVERAGE  LCS_A:  10.40  (   7.09    9.22   14.89 )

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     13     16     17     17     17     18     19     20     20     20     20     21     21     23     25     27     28     28     30     31 
GDT PERCENT_AT   9.22  11.35  12.06  12.06  12.06  12.77  13.48  14.18  14.18  14.18  14.18  14.89  14.89  16.31  17.73  19.15  19.86  19.86  21.28  21.99
GDT RMS_LOCAL    0.27   0.42   0.71   0.71   0.71   1.23   1.68   1.91   1.91   1.91   1.91   2.82   2.82   4.28   4.84   5.20   5.36   5.36   6.40   6.53
GDT RMS_ALL_AT  13.73  13.96  14.28  14.28  14.28  14.64  14.31  14.42  14.42  14.42  14.42  13.43  13.43  10.94  10.00   9.93   9.55   9.55   7.89   7.91

# Checking swapping
#   possible swapping detected:  D   109_A      D   109_A
#   possible swapping detected:  E   122_A      E   122_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    99_A      T    99_A    16.398     0    0.517   0.821    17.273    0.000    0.000
LGA    N   100_A      N   100_A    17.434     0    0.687   1.171    20.382    0.000    0.000
LGA    A   101_A      A   101_A    16.058     0    0.046   0.049    16.688    0.000    0.000
LGA    Y   102_A      Y   102_A    16.221     0    0.615   0.922    18.681    0.000    0.000
LGA    I   103_A      I   103_A    19.602     0    0.622   1.031    22.157    0.000    0.000
LGA    A   104_A      A   104_A    26.214     0    0.631   0.610    28.271    0.000    0.000
LGA    V   105_A      V   105_A    25.932     0    0.040   0.937    27.142    0.000    0.000
LGA    L   106_A      L   106_A    27.869     0    0.057   1.449    29.376    0.000    0.000
LGA    E   107_A      E   107_A    28.823     0    0.691   1.070    29.779    0.000    0.000
LGA    G   108_A      G   108_A    28.170     0    0.621   0.621    30.826    0.000    0.000
LGA    D   109_A      D   109_A    27.659     0    0.520   1.290    32.276    0.000    0.000
LGA    P   110_A      P   110_A    22.143     0    0.682   0.607    25.227    0.000    0.000
LGA    E   111_A      E   111_A    21.806     0    0.641   0.943    27.744    0.000    0.000
LGA    A   112_A      A   112_A    16.343     0    0.638   0.611    18.478    0.000    0.000
LGA    I   113_A      I   113_A    10.631     0    0.613   1.561    12.458    1.905    1.012
LGA    A   114_A      A   114_A    11.769     0    0.062   0.076    14.262    0.000    0.000
LGA    R   115_A      R   115_A    11.426     0    0.115   1.197    15.791    1.429    0.519
LGA    F   116_A      F   116_A     4.496     0    0.603   1.267     7.029   28.929   48.268
LGA    L   117_A      L   117_A     2.900     0    0.728   0.651     5.365   44.167   51.726
LGA    G   118_A      G   118_A     4.237     0    0.572   0.572     4.237   43.452   43.452
LGA    I   119_A      I   119_A     0.924     0    0.113   1.304     4.720   81.786   67.798
LGA    S   120_A      S   120_A     1.243     0    0.068   0.077     1.387   83.690   82.937
LGA    L   121_A      L   121_A     1.626     0    0.064   0.792     3.292   77.143   67.321
LGA    E   122_A      E   122_A     1.167     0    0.038   1.127     4.399   85.952   72.328
LGA    E   123_A      E   123_A     1.028     0    0.063   1.154     4.835   83.690   69.153
LGA    V   124_A      V   124_A     1.116     0    0.056   0.108     1.734   85.952   82.789
LGA    Q   125_A      Q   125_A     0.640     0    0.045   1.168     4.345   90.476   76.349
LGA    E   126_A      E   126_A     0.838     0    0.052   0.223     1.419   90.476   87.460
LGA    I   127_A      I   127_A     1.081     0    0.030   1.303     3.520   85.952   75.893
LGA    I   128_A      I   128_A     1.275     0    0.033   1.292     4.176   83.690   75.952
LGA    D   129_A      D   129_A     1.235     0    0.038   0.174     2.162   83.690   78.333
LGA    A   130_A      A   130_A     0.782     0    0.038   0.042     0.861   90.476   90.476
LGA    A   131_A      A   131_A     1.195     0    0.042   0.056     1.437   83.690   83.238
LGA    R   132_A      R   132_A     1.558     0    0.065   1.092     2.694   75.000   76.926
LGA    K   133_A      K   133_A     1.186     0    0.040   0.458     1.691   81.429   79.577
LGA    A   134_A      A   134_A     1.164     0    0.072   0.071     1.507   79.286   79.714
LGA    V   135_A      V   135_A     2.307     0    0.111   0.120     2.901   64.881   63.741

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     280    280  100.00               141
SUMMARY(RMSD_GDC):     7.834          7.669                  8.966           10.831   10.319

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   37  141    4.0     20    1.91    14.184    12.567     0.993

LGA_LOCAL      RMSD:   1.914  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.418  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   7.834  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.047849 * X  +   0.214157 * Y  +  -0.975627 * Z  +  44.560589
  Y_new =   0.947576 * X  +  -0.299203 * Y  +  -0.112151 * Z  +  -8.914563
  Z_new =  -0.315928 * X  +  -0.929846 * Y  +  -0.188613 * Z  +  73.795074 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.621250  0.321435 -1.770925   [DEG:   92.8908   18.4168 -101.4665 ]
ZXZ: -1.456346  1.760546 -2.814066   [DEG:  -83.4425  100.8719 -161.2341 ]
 
# END of job
