
#######################################################
#                                                     #
#                        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        4.71     7.15
  LCS_AVERAGE:     83.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.71    12.06
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.62    12.61
  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    7   14   16   17   18   19   19   21   23   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    4    6    6    9   11   13   14   16   17   18   19   19   23   23   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    4    6    6    6    7   10   11   13   15   16   18   18   19   20   23   23   25   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   19   23   23   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    8   10   11   11   11   12   13   14   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    8   10   11   11   11   12   13   14   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    8   10   11   11   11   12   13   14   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    8   10   11   11   12   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    8   10   11   11   11   12   13   14   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    8   10   11   11   11   12   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    8   10   12   13   13   14   15   16   16   17   18   20   20   23   23   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8   10   11   11   11   12   13   15   16   17   18   20   20   21   23   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4   10   11   11   12   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   11   12   13   13   14   15   16   16   17   18   19   20   23   23   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      7   11   11   12   13   13   14   15   16   16   17   18   19   20   23   23   23   25   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      7   11   11   12   13   13   14   15   16   16   18   18   20   20   23   23   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   11   12   13   13   14   15   16   16   18   18   20   20   23   23   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     11     12     13     13     14     15     16     16     18     18     20     20     23     23     24     25     25     26 
GDT PERCENT_AT  34.62  42.31  42.31  46.15  50.00  50.00  53.85  57.69  61.54  61.54  69.23  69.23  76.92  76.92  88.46  88.46  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.24   0.37   0.37   0.62   1.00   1.00   1.75   2.22   2.64   2.64   3.98   3.59   4.37   4.23   5.18   5.18   5.55   5.76   5.79   5.99
GDT RMS_ALL_AT  12.28  12.57  12.57  12.61  11.67  11.67  11.50  10.30   9.58   9.58   6.72   8.34   6.91   7.26   6.25   6.25   6.06   6.03   6.05   5.99

# 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    26.051     0    0.280   0.260    28.261    0.000    0.000
LGA    Q     9_D      Q     9_F    20.164     0    0.576   0.487    22.573    0.000    0.000
LGA    K    10_D      K    10_F    20.714     0    0.048   0.635    27.164    0.000    0.000
LGA    L    11_D      L    11_F    17.490     0    0.598   0.627    18.942    0.000    0.000
LGA    N    12_D      N    12_F    13.975     0    0.574   0.562    17.389    0.000    0.000
LGA    S    13_D      S    13_F    12.906     0    0.036   0.070    15.328    0.000    0.000
LGA    W    14_D      W    14_F    14.826     0    0.062   1.491    23.778    0.000    0.000
LGA    D    15_D      D    15_F    10.444     0    0.010   0.164    15.446    6.071    3.036
LGA    V    16_D      V    16_F     4.548     0    0.011   0.052     6.760   27.024   30.612
LGA    F    17_D      F    17_F     9.250     0    0.018   1.279    18.030    5.714    2.078
LGA    G    18_D      G    18_F     6.719     0    0.198   0.198     7.534   28.452   28.452
LGA    N    19_D      N    19_F     1.601     0    0.235   0.991     6.739   54.643   43.333
LGA    W    20_D      W    20_F     6.443     0    0.166   1.304    12.415   20.595    6.429
LGA    F    21_D      F    21_F     4.462     0    0.553   0.927     9.664   45.833   23.290
LGA    D    22_D      D    22_F     2.746     0    0.575   1.353     8.042   62.976   38.690
LGA    L    23_D      L    23_F     2.125     0    0.113   0.909     2.866   68.810   66.905
LGA    A    24_D      A    24_F     1.856     0    0.024   0.027     2.024   72.976   71.333
LGA    S    25_D      S    25_F     1.786     0    0.155   0.723     2.508   79.405   76.032
LGA    W    26_D      W    26_F     1.395     0    0.032   0.219     3.208   83.810   68.707
LGA    I    27_D      I    27_F     0.504     0    0.040   0.093     0.819   95.238   95.238
LGA    K    28_D      K    28_F     0.472     0    0.086   0.615     5.320   97.619   72.540
LGA    Y    29_D      Y    29_F     0.340     0    0.060   0.393     2.398   95.238   83.254
LGA    I    30_D      I    30_F     1.076     0    0.091   0.110     1.958   83.690   79.345
LGA    Q    31_D      Q    31_F     1.796     0    0.023   1.235     6.958   72.976   55.291
LGA    R    32_D      R    32_F     1.426     0    0.464   1.237     2.875   79.286   70.173
LGA    R    33_D      R    33_F     1.691     0    0.196   1.143     7.427   71.071   45.974

# 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):     5.995          5.814                  7.773           44.286   36.951

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.22    58.654    54.482     0.648

LGA_LOCAL      RMSD:   2.216  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.297  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.995  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.069569 * X  +   0.237244 * Y  +   0.968956 * Z  +  25.837543
  Y_new =   0.376264 * X  +   0.893329 * Y  +  -0.245742 * Z  + -83.160423
  Z_new =  -0.923897 * X  +   0.381679 * Y  +  -0.027118 * Z  +   5.458025 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.387967  1.178143  1.641727   [DEG:   79.5246   67.5026   94.0641 ]
ZXZ:  1.322417  1.597918 -1.179032   [DEG:   75.7689   91.5540  -67.5536 ]
 
# END of job
