
#######################################################
#                                                     #
#                        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        4.68     7.05
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.65    12.05
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.50    12.61
  LCS_AVERAGE:     39.35

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   20      0    3    3    3    3    3    4   14   15   17   17   19   19   20   21   23   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   20      3    3    3    6    6   10   13   14   15   17   17   19   19   20   23   23   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      3    4   20      3    4    5    6    6    6    8   11   12   14   15   15   17   17   20   20   23   25   25   26 
LCS_GDT     L    11_D     L    11_F      3   12   20      3    4    5    6   10   11   13   14   15   17   17   19   19   20   23   23   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      7    8   10   11   11   11   13   14   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      7    8   10   11   11   11   13   14   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      7    8   10   11   11   11   13   14   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      7    8   10   11   11   11   13   14   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      7    8   10   11   11   13   14   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      7    8   10   11   11   11   13   14   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      7    8   10   11   11   11   13   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      5    8   10   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8   10   11   11   11   13   14   15   17   17   19   20   21   22   23   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4   10   11   11   12   14   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     10   11   12   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     10   11   12   13   13   13   14   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     10   11   12   13   13   13   14   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     10   11   12   13   13   13   14   15   15   17   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     10   11   12   13   13   13   14   15   15   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      9   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3   11   12   13   13   13   14   15   15   16   18   19   20   21   23   23   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.72  (  39.35   44.38   83.43 )

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     10     11     12     13     13     13     14     15     15     17     18     19     20     21     23     23     24     25     25     26 
GDT PERCENT_AT  38.46  42.31  46.15  50.00  50.00  50.00  53.85  57.69  57.69  65.38  69.23  73.08  76.92  80.77  88.46  88.46  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.29   0.33   0.50   0.97   0.97   0.97   1.71   2.18   2.18   3.64   3.88   4.21   4.18   4.57   5.11   5.11   5.32   5.59   5.59   5.83
GDT RMS_ALL_AT  12.56  12.59  12.61  11.59  11.59  11.59  11.40  10.28  10.28   8.71   7.00   7.45   7.26   6.82   6.14   6.14   6.10   5.87   5.87   5.83

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   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    26.276     0    0.264   1.059    28.418    0.000    0.000
LGA    Q     9_D      Q     9_F    20.200     0    0.558   1.100    22.657    0.000    0.000
LGA    K    10_D      K    10_F    20.748     0    0.965   1.051    27.883    0.000    0.000
LGA    L    11_D      L    11_F    17.265     0    0.578   0.630    18.530    0.000    0.000
LGA    N    12_D      N    12_F    13.665     0    0.578   0.983    14.983    0.119    0.060
LGA    S    13_D      S    13_F    12.668     0    0.024   0.041    14.953    0.000    0.000
LGA    W    14_D      W    14_F    14.864     0    0.082   0.675    23.426    0.000    0.000
LGA    D    15_D      D    15_F    10.367     0    0.688   0.770    12.811    3.571    1.786
LGA    V    16_D      V    16_F     4.512     0    0.111   1.333     6.421   27.976   29.116
LGA    F    17_D      F    17_F     9.260     0    0.072   0.486    17.495    5.714    2.078
LGA    G    18_D      G    18_F     6.980     0    0.156   0.156     7.707   26.905   26.905
LGA    N    19_D      N    19_F     1.504     0    0.897   0.782     7.114   68.929   48.274
LGA    W    20_D      W    20_F     6.337     0    0.200   1.228    16.577   20.595    6.224
LGA    F    21_D      F    21_F     4.364     0    0.576   1.058    11.019   47.262   21.905
LGA    D    22_D      D    22_F     2.871     0    0.566   1.343     7.639   62.976   38.571
LGA    L    23_D      L    23_F     2.185     0    0.094   1.052     4.225   68.810   61.429
LGA    A    24_D      A    24_F     1.832     0    0.055   0.057     2.001   72.976   71.333
LGA    S    25_D      S    25_F     1.798     0    0.132   0.545     2.566   79.405   74.603
LGA    W    26_D      W    26_F     1.370     0    0.039   0.784     4.782   83.810   66.020
LGA    I    27_D      I    27_F     0.480     0    0.024   1.449     4.049   97.619   82.143
LGA    K    28_D      K    28_F     0.475     0    0.067   0.239     1.873   97.619   89.683
LGA    Y    29_D      Y    29_F     0.262     0    0.032   0.294     0.690   97.619   94.444
LGA    I    30_D      I    30_F     0.860     0    0.075   0.740     3.030   88.333   79.881
LGA    Q    31_D      Q    31_F     1.612     0    0.055   1.146     5.969   75.000   56.878
LGA    R    32_D      R    32_F     1.380     0    0.470   1.172     2.506   77.262   73.074
LGA    R    33_D      R    33_F     1.489     0    0.171   1.430     3.780   81.548   62.857

# 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):     5.827          5.667                  7.482           45.540   37.972

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.18    59.615    55.258     0.659

LGA_LOCAL      RMSD:   2.177  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.281  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.827  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.997738 * X  +   0.002111 * Y  +  -0.067196 * Z  + -117.709885
  Y_new =   0.054960 * X  +  -0.601259 * Y  +   0.797162 * Z  + -92.768219
  Z_new =  -0.038720 * X  +  -0.799051 * Y  +  -0.600015 * Z  +   3.337474 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.055029  0.038730 -2.214879   [DEG:    3.1529    2.2190 -126.9032 ]
ZXZ: -3.057497  2.214316 -3.093173   [DEG: -175.1817  126.8710 -177.2258 ]
 
# END of job
