
#######################################################
#                                                     #
#                        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:    24      10_F - 33_F        4.93     5.65
  LCS_AVERAGE:     91.72

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      11_F - 22_F        1.57    10.00
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        1.07    16.16
  LCS_AVERAGE:     42.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      22_F - 32_F        0.89    15.75
  LONGEST_CONTINUOUS_SEGMENT:    11      23_F - 33_F        0.96    16.72
  LCS_AVERAGE:     35.06

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   22      0    3    3    3    3    4    4    7    8   15   17   19   19   22   23   23   25   26   26   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   22      3    3    5    5    5    9   11   13   14   15   18   19   21   22   23   24   25   26   26   26 
LCS_GDT     K    10_D     K    10_F      4    4   24      3    3    5    5    5    6   10   12   14   15   18   19   21   22   23   24   25   26   26   26 
LCS_GDT     L    11_D     L    11_F      4   12   24      3    3    6    8   10   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     N    12_D     N    12_F      9   12   24      4    8    9   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     S    13_D     S    13_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     W    14_D     W    14_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     D    15_D     D    15_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     V    16_D     V    16_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     F    17_D     F    17_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     G    18_D     G    18_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     N    19_D     N    19_F      9   12   24      4    8   10   11   11   11   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     W    20_D     W    20_F      9   12   24      4    8   10   11   11   11   12   13   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     F    21_D     F    21_F      9   12   24      3    3   10   11   11   11   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     D    22_D     D    22_F     11   12   24      6    9   11   12   12   12   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     L    23_D     L    23_F     11   12   24      6    9   11   12   12   12   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     A    24_D     A    24_F     11   12   24      6    9   11   12   12   12   13   14   14   16   17   20   21   22   23   24   25   26   26   26 
LCS_GDT     S    25_D     S    25_F     11   12   24      4    9   11   12   12   12   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     W    26_D     W    26_F     11   12   24      6    9   11   12   12   12   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     I    27_D     I    27_F     11   12   24      6    9   11   12   12   12   13   14   14   15   17   18   21   22   23   24   25   26   26   26 
LCS_GDT     K    28_D     K    28_F     11   12   24      6    9   11   12   12   12   13   14   14   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     Y    29_D     Y    29_F     11   12   24      3    9   11   12   12   12   13   14   16   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     I    30_D     I    30_F     11   12   24      4    9   11   12   12   12   13   14   14   15   17   18   21   22   23   24   25   26   26   26 
LCS_GDT     Q    31_D     Q    31_F     11   12   24      4    8   11   12   12   12   13   14   14   15   16   17   21   21   23   24   25   26   26   26 
LCS_GDT     R    32_D     R    32_F     11   12   24      4    8   11   12   12   12   13   14   15   16   18   20   21   22   23   24   25   26   26   26 
LCS_GDT     R    33_D     R    33_F     11   12   24      3    6    6   12   12   12   13   14   15   16   18   20   21   22   23   24   25   26   26   26 
LCS_AVERAGE  LCS_A:  56.41  (  35.06   42.46   91.72 )

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      6      9     11     12     12     12     13     14     16     16     18     20     21     22     23     24     25     26     26     26 
GDT PERCENT_AT  23.08  34.62  42.31  46.15  46.15  46.15  50.00  53.85  61.54  61.54  69.23  76.92  80.77  84.62  88.46  92.31  96.15 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.50   0.89   1.07   1.07   1.07   1.80   2.31   3.17   3.17   3.71   4.02   4.23   4.44   4.67   4.93   5.15   5.41   5.41   5.41
GDT RMS_ALL_AT  14.29  14.83  15.75  16.16  16.16  16.16  14.42  14.15   6.70   6.70   5.81   5.95   5.95   5.95   6.02   5.65   5.48   5.41   5.41   5.41

# Checking swapping
#   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    33.133     0    0.230   0.233    35.432    0.000    0.000
LGA    Q     9_D      Q     9_F    29.766     0    0.561   1.232    33.000    0.000    0.000
LGA    K    10_D      K    10_F    28.321     0    0.076   0.813    34.573    0.000    0.000
LGA    L    11_D      L    11_F    22.379     0    0.595   1.259    24.681    0.000    0.000
LGA    N    12_D      N    12_F    20.386     0    0.584   1.035    25.672    0.000    0.000
LGA    S    13_D      S    13_F    20.642     0    0.070   0.735    24.359    0.000    0.000
LGA    W    14_D      W    14_F    19.396     0    0.120   0.201    22.369    0.000    0.000
LGA    D    15_D      D    15_F    14.135     0    0.025   1.177    16.952    0.119    0.060
LGA    V    16_D      V    16_F    10.487     0    0.027   1.005    12.553    0.714    0.408
LGA    F    17_D      F    17_F    13.261     0    0.042   0.965    21.018    0.000    0.000
LGA    G    18_D      G    18_F     9.486     0    0.141   0.141    10.957   10.238   10.238
LGA    N    19_D      N    19_F     3.349     0    0.243   0.568     5.812   41.190   45.774
LGA    W    20_D      W    20_F     6.904     0    0.181   1.045    17.473   15.000    4.320
LGA    F    21_D      F    21_F     4.933     0    0.566   1.045    10.243   37.976   18.225
LGA    D    22_D      D    22_F     2.241     0    0.573   1.046     7.493   73.214   44.702
LGA    L    23_D      L    23_F     1.297     0    0.107   1.138     4.263   81.429   71.905
LGA    A    24_D      A    24_F     1.283     0    0.044   0.054     1.587   77.143   78.000
LGA    S    25_D      S    25_F     2.161     0    0.154   0.552     3.140   70.833   65.079
LGA    W    26_D      W    26_F     1.964     0    0.028   0.303     4.087   72.857   56.905
LGA    I    27_D      I    27_F     1.025     0    0.037   1.355     3.212   83.690   75.595
LGA    K    28_D      K    28_F     0.863     0    0.141   0.459     3.093   90.476   74.868
LGA    Y    29_D      Y    29_F     1.597     0    0.047   0.177     2.840   77.143   65.079
LGA    I    30_D      I    30_F     1.743     0    0.034   0.144     3.856   79.286   63.869
LGA    Q    31_D      Q    31_F     2.131     0    0.037   1.311     8.383   64.881   42.963
LGA    R    32_D      R    32_F     2.135     0    0.499   1.277     4.164   70.833   55.931
LGA    R    33_D      R    33_F     2.357     0    0.122   1.074     4.563   62.976   53.723

# 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):     5.406          5.117                  7.366           38.846   31.832

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     14    2.31    56.731    53.242     0.582

LGA_LOCAL      RMSD:   2.306  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.145  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.406  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.230375 * X  +   0.713862 * Y  +   0.661308 * Z  +  71.582390
  Y_new =   0.771703 * X  +  -0.548013 * Y  +   0.322732 * Z  + -56.764576
  Z_new =   0.592791 * X  +   0.435985 * Y  +  -0.677138 * Z  + -36.873196 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.280691 -0.634521  2.569543   [DEG:   73.3782  -36.3554  147.2240 ]
ZXZ:  2.024814  2.314662  0.936655   [DEG:  116.0133  132.6204   53.6664 ]
 
# END of job
