
#######################################################
#                                                     #
#                        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     7.13
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.71    12.11
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.60    12.66
  LCS_AVERAGE:     39.79

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    7   14   16   17   18   19   19   22   23   24   24   26   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   20      3    3    4    6    6    8   10   13   14   16   17   18   19   19   23   23   24   24   26   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    4    6    6    6    7   10   11   13   15   15   17   19   20   20   23   24   26   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    4    6    9   11   12   13   14   16   17   18   19   20   23   23   24   24   26   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    8    9   11   11   11   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    8    9   11   11   11   12   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    8    9   13   13   13   14   15   16   16   17   20   20   21   23   23   24   24   26   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8    9   11   11   11   12   13   15   16   17   20   20   21   22   23   24   24   26   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4    9   11   11   12   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   12   13   13   13   14   15   16   16   17   18   19   21   23   23   24   24   26   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      9   11   12   13   13   13   14   15   16   16   17   18   19   20   23   23   23   24   26   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      8   11   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   12   13   13   13   14   15   16   16   18   20   20   21   23   23   24   24   26   26 
LCS_AVERAGE  LCS_A:  55.87  (  39.79   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      9     11     12     13     13     13     14     15     16     16     18     20     20     21     23     23     24     24     26     26 
GDT PERCENT_AT  34.62  42.31  46.15  50.00  50.00  50.00  53.85  57.69  61.54  61.54  69.23  76.92  76.92  80.77  88.46  88.46  92.31  92.31 100.00 100.00
GDT RMS_LOCAL    0.23   0.37   0.60   0.97   0.97   0.97   1.75   2.22   2.62   2.62   3.94   4.32   4.32   4.54   5.18   5.18   5.51   5.41   5.97   5.97
GDT RMS_ALL_AT  12.36  12.65  12.66  11.76  11.76  11.76  11.58  10.36   9.65   9.65   6.70   6.89   6.89   6.96   6.25   6.25   6.03   6.24   5.97   5.97

# Checking swapping
#   possible swapping detected:  F    21_D      F    21_F
#   possible swapping detected:  D    22_D      D    22_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    26.190     0    0.280   0.260    28.434    0.000    0.000
LGA    Q     9_D      Q     9_F    20.412     0    0.577   0.488    22.787    0.000    0.000
LGA    K    10_D      K    10_F    20.991     0    0.048   0.635    27.609    0.000    0.000
LGA    L    11_D      L    11_F    17.611     0    0.597   0.628    19.071    0.000    0.000
LGA    N    12_D      N    12_F    14.034     0    0.572   0.560    17.430    0.000    0.000
LGA    S    13_D      S    13_F    13.037     0    0.035   0.073    15.522    0.000    0.000
LGA    W    14_D      W    14_F    14.824     0    0.062   1.493    23.600    0.000    0.000
LGA    D    15_D      D    15_F    10.417     0    0.010   0.164    15.380    6.071    3.036
LGA    V    16_D      V    16_F     4.604     0    0.001   0.050     6.792   27.024   29.116
LGA    F    17_D      F    17_F     9.197     0    0.031   1.170    18.043    6.429    2.338
LGA    G    18_D      G    18_F     6.591     0    0.212   0.212     7.445   30.952   30.952
LGA    N    19_D      N    19_F     1.600     0    0.232   0.989     6.761   56.548   43.036
LGA    W    20_D      W    20_F     6.463     0    0.153   1.304    12.284   20.595    6.327
LGA    F    21_D      F    21_F     4.484     0    0.610   1.252    11.665   45.833   19.957
LGA    D    22_D      D    22_F     2.789     0    0.570   1.356     8.088   62.976   38.690
LGA    L    23_D      L    23_F     2.120     0    0.115   0.907     2.854   68.810   66.905
LGA    A    24_D      A    24_F     1.835     0    0.026   0.028     2.015   75.000   72.952
LGA    S    25_D      S    25_F     1.751     0    0.183   0.730     2.486   77.143   75.794
LGA    W    26_D      W    26_F     1.340     0    0.033   0.232     3.182   85.952   69.932
LGA    I    27_D      I    27_F     0.498     0    0.037   0.090     0.774   97.619   96.429
LGA    K    28_D      K    28_F     0.458     0    0.097   0.611     5.252   97.619   72.540
LGA    Y    29_D      Y    29_F     0.306     0    0.017   1.242     7.623   97.619   62.183
LGA    I    30_D      I    30_F     1.077     0    0.074   0.113     1.985   83.690   79.345
LGA    Q    31_D      Q    31_F     1.821     0    0.032   1.238     6.958   72.976   55.291
LGA    R    32_D      R    32_F     1.446     0    0.486   1.237     3.057   77.262   69.481
LGA    R    33_D      R    33_F     1.581     0    0.587   1.267     5.448   77.143   55.065

# 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):     5.966          5.794                  7.742           44.895   36.514

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.22    59.615    55.393     0.646

LGA_LOCAL      RMSD:   2.221  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.363  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.966  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.538898 * X  +   0.710742 * Y  +  -0.452145 * Z  +  26.838875
  Y_new =   0.109368 * X  +   0.591243 * Y  +   0.799043 * Z  + -82.765923
  Z_new =   0.835241 * X  +   0.381152 * Y  +  -0.396352 * Z  +   1.399717 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.941364 -0.988571  2.375742   [DEG:  168.5277  -56.6410  136.1200 ]
ZXZ: -2.626656  1.978337  1.142684   [DEG: -150.4963  113.3503   65.4710 ]
 
# END of job
