
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.86     7.29
  LCS_AVERAGE:     83.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      11_F - 22_F        1.83    11.29
  LONGEST_CONTINUOUS_SEGMENT:    12      21_F - 32_F        1.80    12.39
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        1.43    13.99
  LCS_AVERAGE:     42.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      22_F - 32_F        0.45    12.96
  LCS_AVERAGE:     31.95

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     L     8_D     L     8_F      3    3   19      0    3    3    3    3    3    6    8   14   15   16   17   19   20   20   23   24   25   25   25 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    5    5    5    8   10   12   14   15   16   17   19   20   22   23   24   25   25   25 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    5    5    5    7    7   11   12   15   15   17   19   21   22   23   24   25   25   25 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    6    7    9   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     N    12_D     N    12_F      8   12   22      4    7    8   11   11   11   12   13   14   15   16   18   20   21   22   23   24   25   25   25 
LCS_GDT     S    13_D     S    13_F      8   12   22      4    7    8   11   11   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     W    14_D     W    14_F      8   12   22      4    7    8   11   11   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     D    15_D     D    15_F      8   12   22      4    7    8   11   11   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     V    16_D     V    16_F      8   12   22      4    7    8   11   11   11   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     F    17_D     F    17_F      8   12   22      3    7    8   11   11   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     G    18_D     G    18_F      8   12   22      3    7    8   11   11   11   12   13   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     N    19_D     N    19_F      8   12   22      3    7    8   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     W    20_D     W    20_F      8   12   22      3    4    8   11   11   11   12   13   14   15   17   18   20   21   21   23   24   25   25   25 
LCS_GDT     F    21_D     F    21_F      5   12   22      3    4    7   11   11   11   12   14   14   15   16   18   20   21   21   23   24   25   25   25 
LCS_GDT     D    22_D     D    22_F     11   12   22      9   11   11   11   12   12   12   14   14   15   16   17   19   21   22   23   24   25   25   25 
LCS_GDT     L    23_D     L    23_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     A    24_D     A    24_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     S    25_D     S    25_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     W    26_D     W    26_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     I    27_D     I    27_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     K    28_D     K    28_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     Y    29_D     Y    29_F     11   12   22      9   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     I    30_D     I    30_F     11   12   22      9   11   11   11   12   12   12   14   14   15   16   18   19   21   22   22   24   25   25   25 
LCS_GDT     Q    31_D     Q    31_F     11   12   22      9   11   11   11   12   12   12   14   14   15   16   17   19   20   22   22   23   23   24   25 
LCS_GDT     R    32_D     R    32_F     11   12   22      7   11   11   11   12   12   12   14   14   15   17   18   20   21   22   23   24   25   25   25 
LCS_GDT     R    33_D     R    33_F      3   12   22      0    3    3    6    7   10   12   12   14   15   17   18   20   21   21   23   24   25   25   25 
LCS_AVERAGE  LCS_A:  52.51  (  31.95   42.46   83.14 )

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      9     11     11     11     12     12     12     14     14     15     17     18     20     21     22     23     24     25     25     25 
GDT PERCENT_AT  34.62  42.31  42.31  42.31  46.15  46.15  46.15  53.85  53.85  57.69  65.38  69.23  76.92  80.77  84.62  88.46  92.31  96.15  96.15  96.15
GDT RMS_LOCAL    0.30   0.45   0.45   0.45   1.07   1.07   1.07   2.37   2.28   2.67   3.84   4.01   4.38   4.56   5.18   5.30   5.53   5.73   5.73   5.73
GDT RMS_ALL_AT  12.61  12.96  12.96  12.96  11.75  11.75  11.75  10.32  12.36  12.46   7.10   7.84   6.60   6.64   6.39   6.16   6.16   6.07   6.07   6.07

# Checking swapping
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    25.178     0    0.255   0.274    27.679    0.000    0.000
LGA    Q     9_D      Q     9_F    20.696     0    0.551   1.156    22.878    0.000    0.000
LGA    K    10_D      K    10_F    21.204     0    0.039   1.143    24.099    0.000    0.000
LGA    L    11_D      L    11_F    16.750     0    0.585   0.508    18.376    0.000    0.000
LGA    N    12_D      N    12_F    13.616     0    0.561   1.392    14.693    0.000    0.000
LGA    S    13_D      S    13_F    13.690     0    0.049   0.742    17.197    0.000    0.000
LGA    W    14_D      W    14_F    14.551     0    0.091   0.174    18.809    0.000    0.000
LGA    D    15_D      D    15_F     9.765     0    0.047   0.201    14.461    8.810    4.405
LGA    V    16_D      V    16_F     4.422     0    0.045   1.156     6.398   29.405   28.299
LGA    F    17_D      F    17_F     8.945     0    0.623   1.127    17.450    8.571    3.117
LGA    G    18_D      G    18_F     7.014     0    0.292   0.292     7.807   24.405   24.405
LGA    N    19_D      N    19_F     2.104     0    0.242   0.225     7.644   52.619   37.798
LGA    W    20_D      W    20_F     6.085     0    0.185   1.203    15.919   22.262    6.735
LGA    F    21_D      F    21_F     4.780     0    0.562   1.019    10.116   42.500   20.173
LGA    D    22_D      D    22_F     2.490     0    0.567   0.821     7.799   66.786   41.131
LGA    L    23_D      L    23_F     2.379     0    0.103   1.206     5.366   64.762   58.988
LGA    A    24_D      A    24_F     2.324     0    0.039   0.051     2.496   66.786   66.381
LGA    S    25_D      S    25_F     1.866     0    0.158   0.712     2.528   77.381   73.254
LGA    W    26_D      W    26_F     1.240     0    0.039   0.289     3.570   85.952   67.313
LGA    I    27_D      I    27_F     0.631     0    0.035   0.066     1.291   95.238   91.786
LGA    K    28_D      K    28_F     0.750     0    0.065   1.036     3.293   90.476   82.963
LGA    Y    29_D      Y    29_F     0.449     0    0.038   0.502     2.024   92.976   85.675
LGA    I    30_D      I    30_F     1.107     0    0.064   1.610     5.302   81.548   68.750
LGA    Q    31_D      Q    31_F     1.931     0    0.119   1.091     6.450   70.833   54.180
LGA    R    32_D      R    32_F     1.899     0    0.403   1.631     7.768   56.548   44.545
LGA    R    33_D      R    33_F     7.120     0    0.181   1.197    17.993   10.952    4.242

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     6.032          5.812                  7.493           40.339   33.236

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     14    2.37    56.731    51.926     0.566

LGA_LOCAL      RMSD:   2.373  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.318  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.032  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.505229 * X  +  -0.457956 * Y  +  -0.731451 * Z  +  44.368103
  Y_new =  -0.792560 * X  +  -0.581589 * Y  +  -0.183310 * Z  + -62.473644
  Z_new =  -0.341456 * X  +   0.672333 * Y  +  -0.656793 * Z  +  13.846420 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.003284  0.348465  2.344503   [DEG:  -57.4839   19.9656  134.3302 ]
ZXZ: -1.325242  2.287354 -0.469922   [DEG:  -75.9308  131.0557  -26.9245 ]
 
# END of job
