
#######################################################
#                                                     #
#                        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   40 (  313),  selected   40 , name one
# Molecule2: number of CA atoms  207 ( 1517),  selected   40 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      11_B - 36_B        4.77    18.76
  LCS_AVERAGE:     10.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      21_B - 30_B        1.59    25.39
  LCS_AVERAGE:      3.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      21_B - 28_B        0.51    25.66
  LCS_AVERAGE:      2.17

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   40
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     E    11_B     E    11_B      3    4   26      3    3    3    3   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     R    12_B     R    12_B      3    5   26      3    3    4    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     F    13_B     F    13_B      4    6   26      4    4    4    4    6   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     L    14_B     L    14_B      4    6   26      4    4    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     A    15_B     A    15_B      4    6   26      4    4    4    5    7   10   12   12   15   17   19   21   23   24   24   25   28   28   29   29 
LCS_GDT     G    16_B     G    16_B      4    6   26      4    4    4    5    7   10   12   12   14   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     D    17_B     D    17_B      4    6   26      3    4    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     V    18_B     V    18_B      4    6   26      3    4    4    5    6   10   12   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     T    19_B     T    19_B      4    4   26      4    4    4    4    7    9   12   12   14   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     I    20_B     I    20_B      4    9   26      4    4    4    6    9   10   12   12   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     V    21_B     V    21_B      8   10   26      7    8    8    9    9   10   12   12   13   16   17   18   21   24   24   25   26   28   29   29 
LCS_GDT     L    22_B     L    22_B      8   10   26      7    8    8    9    9   10   12   12   16   18   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     L    23_B     L    23_B      8   10   26      7    8    8    9    9   11   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     I    24_B     I    24_B      8   10   26      7    8    8    9   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     A    25_B     A    25_B      8   10   26      7    8    8    9    9   10   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     E    26_B     E    26_B      8   10   26      7    8    8    9   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     S    27_B     S    27_B      8   10   26      7    8    8    9    9   10   11   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     H    28_B     H    28_B      8   10   26      3    8    8    9    9   10   10   12   14   17   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     D    29_B     D    29_B      3   10   26      3    3    5    7    9    9   10   10   11   13   13   14   16   19   21   25   28   28   29   29 
LCS_GDT     A    30_B     A    30_B      3   10   26      3    3    8    9    9   10   10   11   12   16   18   18   22   24   24   25   28   28   29   29 
LCS_GDT     P    31_B     P    31_B      3    8   26      3    3    4    6    9   10   10   12   14   17   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     Y    32_B     Y    32_B      4    8   26      3    3    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     R    33_B     R    33_B      4    8   26      3    3    5    8    9   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     L    34_B     L    34_B      4    8   26      3    3    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     A    35_B     A    35_B      4    8   26      3    3    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     N    36_B     N    36_B      4    8   26      3    3    5    8   10   12   13   14   16   19   20   22   23   24   24   25   28   28   29   29 
LCS_GDT     P    37_B     P    37_B      4    5   16      3    3    4    4    5    5    5    7    8   10   11   13   15   20   23   25   28   28   29   29 
LCS_GDT     E    38_B     E    38_B      4    5   16      3    3    4    4    5    7    7    9    9   10   11   13   15   16   21   25   28   28   29   29 
LCS_GDT     D    39_B     D    39_B      3    5   15      3    3    3    4    5    7    7    9    9   10   11   12   17   19   23   25   28   28   29   29 
LCS_GDT     P    40_B     P    40_B      3    5   12      3    3    3    4    5    7    7    9    9   10   11   11   11   11   12   13   14   16   20   22 
LCS_GDT     E    41_B     E    41_B      3    5   12      3    3    3    4    5    5    5    8    9   10   11   11   11   11   12   13   13   16   20   22 
LCS_GDT     A    42_B     A    42_B      3    6   12      3    3    5    6    6    7    7    9    9   10   11   11   11   11   12   13   13   16   19   22 
LCS_GDT     D    43_B     D    43_B      4    6   12      3    4    5    6    6    7    7    9    9   10   11   11   11   11   12   12   13   13   13   14 
LCS_GDT     L    44_B     L    44_B      4    6   12      3    4    5    6    6    7    7    9    9   10   11   11   11   11   12   12   13   13   13   14 
LCS_GDT     S    45_B     S    45_B      4    6   12      3    4    5    6    6    7    7    9    9   10   11   11   11   11   12   12   13   13   13   14 
LCS_GDT     D    46_B     D    46_B      4    6   12      3    4    5    6    6    6    7    9    9   10   11   11   11   11   12   12   13   13   13   14 
LCS_GDT     E    47_B     E    47_B      4    6   12      3    3    5    6    6    6    6    9    9   10   11   11   11   11   12   12   13   13   13   14 
LCS_GDT     Q    48_B     Q    48_B      3    4   12      3    3    3    3    4    4    5    5    7    7    9    9   10   11   11   12   13   13   13   14 
LCS_GDT     L    49_B     L    49_B      3    3   12      3    3    3    3    4    4    5    5    6    7    9    9    9    9   10   12   13   13   13   14 
LCS_GDT     E    50_B     E    50_B      3    3   10      3    3    3    3    4    4    4    4    5    7    9    9    9    9   10   12   13   13   13   14 
LCS_AVERAGE  LCS_A:   5.27  (   2.17    3.35   10.30 )

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      7      8      8      9     10     12     13     14     16     19     20     22     23     24     24     25     28     28     29     29 
GDT PERCENT_AT   3.38   3.86   3.86   4.35   4.83   5.80   6.28   6.76   7.73   9.18   9.66  10.63  11.11  11.59  11.59  12.08  13.53  13.53  14.01  14.01
GDT RMS_LOCAL    0.30   0.51   0.51   0.91   1.91   2.14   2.29   2.48   2.90   3.44   3.59   3.99   4.13   4.33   4.33   4.54   5.37   5.27   5.54   5.54
GDT RMS_ALL_AT  26.29  25.66  25.66  24.84  19.18  19.30  19.54  19.42  19.06  19.03  19.18  18.70  18.74  18.73  18.73  18.88  17.86  18.42  17.96  17.96

# Checking swapping
#   possible swapping detected:  D    29_B      D    29_B
#   possible swapping detected:  E    41_B      E    41_B
#   possible swapping detected:  D    43_B      D    43_B
#   possible swapping detected:  D    46_B      D    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    11_B      E    11_B     2.240     0    0.621   1.489     8.372   58.452   43.016
LGA    R    12_B      R    12_B     1.449     0    0.033   1.528    12.286   77.143   40.563
LGA    F    13_B      F    13_B     3.116     0    0.579   1.242    11.734   65.238   28.182
LGA    L    14_B      L    14_B     1.917     3    0.071   0.082     4.798   57.262   34.881
LGA    A    15_B      A    15_B     5.639     0    0.162   0.159     7.745   21.786   20.857
LGA    G    16_B      G    16_B     5.649     0    0.296   0.296     5.649   29.048   29.048
LGA    D    17_B      D    17_B     2.131     0    0.511   1.138     5.175   55.595   48.512
LGA    V    18_B      V    18_B     5.430     0    0.657   0.603     8.959   29.286   18.231
LGA    T    19_B      T    19_B     6.451     0    0.693   1.322     9.451   20.476   13.333
LGA    I    20_B      I    20_B     6.163     0    0.050   0.888     7.313   15.238   14.464
LGA    V    21_B      V    21_B     8.415     0    0.576   0.856    11.879   12.857    7.347
LGA    L    22_B      L    22_B     6.403     0    0.084   0.998     8.413   26.429   16.845
LGA    L    23_B      L    23_B     4.000     0    0.063   0.204     7.908   51.190   35.119
LGA    I    24_B      I    24_B     1.505     0    0.051   1.680     4.562   73.333   65.060
LGA    A    25_B      A    25_B     3.713     0    0.065   0.084     5.309   47.381   43.143
LGA    E    26_B      E    26_B     2.432     0    0.052   1.141     5.534   52.738   47.619
LGA    S    27_B      S    27_B     4.671     0    0.560   0.857     6.459   32.976   29.206
LGA    H    28_B      H    28_B     6.563     0    0.120   1.298    10.965   12.381    9.429
LGA    D    29_B      D    29_B     8.864     0    0.358   1.280    12.466    3.929    1.964
LGA    A    30_B      A    30_B     7.724     0    0.165   0.197     7.724   13.810   13.048
LGA    P    31_B      P    31_B     7.012     0    0.115   0.406    11.569   18.690   10.884
LGA    Y    32_B      Y    32_B     1.594     0    0.698   1.256    12.134   65.119   34.206
LGA    R    33_B      R    33_B     2.731     0    0.215   1.589    15.633   63.214   27.186
LGA    L    34_B      L    34_B     1.728     0    0.136   1.186     6.767   75.119   51.845
LGA    A    35_B      A    35_B     2.030     0    0.613   0.607     3.258   65.119   63.524
LGA    N    36_B      N    36_B     2.515     3    0.244   0.255     6.692   40.357   25.595
LGA    P    37_B      P    37_B     9.266     0    0.547   0.512    10.818    3.810    4.286
LGA    E    38_B      E    38_B    11.295     4    0.679   0.627    12.029    0.000    0.000
LGA    D    39_B      D    39_B    13.327     0    0.339   0.440    15.892    0.000    0.000
LGA    P    40_B      P    40_B    19.097     0    0.634   0.594    21.163    0.000    0.000
LGA    E    41_B      E    41_B    23.303     0    0.652   1.160    28.567    0.000    0.000
LGA    A    42_B      A    42_B    22.232     0    0.635   0.570    24.821    0.000    0.000
LGA    D    43_B      D    43_B    26.628     0    0.312   1.401    29.261    0.000    0.000
LGA    L    44_B      L    44_B    31.332     0    0.029   0.961    33.904    0.000    0.000
LGA    S    45_B      S    45_B    36.567     0    0.081   0.734    38.787    0.000    0.000
LGA    D    46_B      D    46_B    40.388     0    0.602   1.198    44.182    0.000    0.000
LGA    E    47_B      E    47_B    44.707     0    0.625   0.943    49.298    0.000    0.000
LGA    Q    48_B      Q    48_B    44.016     0    0.648   0.718    45.299    0.000    0.000
LGA    L    49_B      L    49_B    41.810     0    0.621   1.097    45.030    0.000    0.000
LGA    E    50_B      E    50_B    48.199     4    0.644   0.605    50.237    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       40     160    160  100.00     299    299  100.00               207
SUMMARY(RMSD_GDC):    14.397         14.583                 14.909            5.256    3.756

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   40  207    4.0     14    2.48     6.763     6.123     0.542

LGA_LOCAL      RMSD:   2.485  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.418  Number of assigned atoms:   40 
Std_ASGN_ATOMS RMSD:  14.397  Standard rmsd on all 40 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.464150 * X  +   0.688233 * Y  +  -0.557585 * Z  +  -7.071025
  Y_new =   0.635205 * X  +   0.697352 * Y  +   0.331985 * Z  + -52.122379
  Z_new =   0.617316 * X  +  -0.200090 * Y  +  -0.760845 * Z  +  34.176357 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.201837 -0.665326 -2.884432   [DEG:  126.1559  -38.1204 -165.2658 ]
ZXZ: -2.107826  2.435411  1.884240   [DEG: -120.7695  139.5388  107.9590 ]
 
# END of job
