
#######################################################
#                                                     #
#                        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        4.91     7.47
  LCS_AVERAGE:     83.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.75    12.35
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.58    12.82
  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   19      0    3    3    3    3    3    4    9   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    5    5    6   10   12   13   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    5    5    6    6    8   10   11   14   15   16   19   20   22   22   24   25   25   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    5    5    9   11   12   13   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    9    9   11   11   11   12   13   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    9    9   11   11   11   12   13   15   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    9    9   11   11   11   12   13   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    9    9   11   11   11   12   13   14   16   16   17   19   20   22   22   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    9    9   11   11   11   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    9    9   11   11   11   12   13   15   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    9    9   11   11   11   12   13   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    9   11   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    9    9   11   11   11   12   14   15   16   16   18   19   20   22   22   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4    9   11   11   11   13   15   16   16   18   18   19   20   21   22   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   12   13   13   13   14   15   16   16   18   18   19   20   21   22   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      8   11   12   13   13   13   14   15   16   16   18   18   19   20   21   22   24   24   24   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      7   11   12   13   13   13   14   15   16   16   18   18   19   20   22   22   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    6   12   13   13   13   14   15   16   16   18   18   19   20   21   22   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.77  (  39.79   44.38   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     12     13     13     13     14     15     16     16     18     18     19     20     22     22     24     25     25     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  69.23  73.08  76.92  84.62  84.62  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.26   0.42   0.58   1.02   1.02   1.02   1.87   2.27   2.72   2.72   3.68   3.43   4.01   4.60   5.25   5.07   5.57   5.90   5.90   6.14
GDT RMS_ALL_AT  12.47  12.80  12.82  11.81  11.81  11.81  10.24  10.47   9.78   9.78   8.60   9.88   8.04   7.63   6.43   6.69   6.27   6.19   6.19   6.14

# Checking swapping
#   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    26.959     0    0.278   0.260    29.875    0.000    0.000
LGA    Q     9_D      Q     9_F    20.589     0    0.575   0.492    23.187    0.000    0.000
LGA    K    10_D      K    10_F    20.364     0    0.047   0.639    25.870    0.000    0.000
LGA    L    11_D      L    11_F    17.608     0    0.602   0.629    18.738    0.000    0.000
LGA    N    12_D      N    12_F    14.598     0    0.564   0.557    18.608    0.000    0.000
LGA    S    13_D      S    13_F    12.876     0    0.026   0.078    15.064    0.000    0.000
LGA    W    14_D      W    14_F    15.046     0    0.048   1.501    24.539    0.000    0.000
LGA    D    15_D      D    15_F    10.865     0    0.012   0.166    16.201    5.119    2.560
LGA    V    16_D      V    16_F     4.589     0    0.000   0.042     6.997   27.024   30.612
LGA    F    17_D      F    17_F     9.253     0    0.012   1.215    18.075    5.714    2.078
LGA    G    18_D      G    18_F     7.007     0    0.192   0.192     7.736   26.071   26.071
LGA    N    19_D      N    19_F     1.559     0    0.250   0.996     6.649   54.643   43.333
LGA    W    20_D      W    20_F     6.391     0    0.157   1.302    12.395   20.595    6.497
LGA    F    21_D      F    21_F     4.734     0    0.558   0.933     9.809   42.500   20.866
LGA    D    22_D      D    22_F     2.562     0    0.576   1.351     7.785   64.881   41.548
LGA    L    23_D      L    23_F     2.246     0    0.097   1.043     4.808   66.786   61.667
LGA    A    24_D      A    24_F     2.032     0    0.021   0.026     2.197   68.810   68.000
LGA    S    25_D      S    25_F     1.821     0    0.168   0.721     2.493   75.119   74.444
LGA    W    26_D      W    26_F     1.451     0    0.048   1.306     6.576   81.548   58.061
LGA    I    27_D      I    27_F     0.560     0    0.026   0.095     0.942   95.238   94.048
LGA    K    28_D      K    28_F     0.482     0    0.093   0.605     5.252   97.619   72.540
LGA    Y    29_D      Y    29_F     0.326     0    0.035   1.264     7.399   92.857   62.421
LGA    I    30_D      I    30_F     1.109     0    0.072   0.688     3.199   83.690   75.476
LGA    Q    31_D      Q    31_F     1.883     0    0.016   1.229     7.046   72.976   54.921
LGA    R    32_D      R    32_F     1.531     0    0.467   1.218     3.205   72.976   67.922
LGA    R    33_D      R    33_F     1.584     0    0.127   0.919    10.981   75.238   37.056

# 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):     6.141          5.967                  7.786           43.439   34.620

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.27    58.654    54.769     0.633

LGA_LOCAL      RMSD:   2.271  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.473  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.141  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.040881 * X  +   0.036307 * Y  +   0.998504 * Z  +  27.847954
  Y_new =   0.170863 * X  +   0.984873 * Y  +  -0.028816 * Z  + -82.950279
  Z_new =  -0.984446 * X  +   0.169430 * Y  +  -0.046466 * Z  +   8.464115 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.805640  1.394194  1.838462   [DEG:  103.4556   79.8814  105.3361 ]
ZXZ:  1.541945  1.617279 -1.400359   [DEG:   88.3470   92.6632  -80.2347 ]
 
# END of job
