
#######################################################
#                                                     #
#                        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   30 (  244),  selected   30 , name one
# Molecule2: number of CA atoms  124 (  971),  selected   30 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       1_A - 30_A        4.71     4.71
  LCS_AVERAGE:     24.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      13_A - 26_A        1.89    10.19
  LONGEST_CONTINUOUS_SEGMENT:    14      14_A - 27_A        1.99    10.45
  LCS_AVERAGE:      9.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       8_A - 16_A        1.00     6.59
  LCS_AVERAGE:      4.78

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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     M     1_F     M     1_A      4    5   30      3    4    4    4    5    7    9   11   13   17   18   21   27   29   29   30   30   30   30   30 
LCS_GDT     F     2_F     F     2_A      4    5   30      3    4    4    4    5    7   11   12   17   20   23   25   28   29   29   30   30   30   30   30 
LCS_GDT     T     3_F     T     3_A      4    5   30      3    4    4    4    5    7    9   11   18   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     G     4_F     G     4_A      4    5   30      3    4    4    4    5    9   12   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     W     5_F     W     5_A      4    6   30      3    3    4    4    5    7   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     S     6_F     S     6_A      5   13   30      3    4    7   11   13   14   16   20   21   22   24   26   28   29   29   30   30   30   30   30 
LCS_GDT     P     7_F     P     7_A      5   13   30      3    4    8   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     F     8_F     F     8_A      9   13   30      3    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     K     9_F     K     9_A      9   13   30      4    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     Y    10_F     Y    10_A      9   13   30      4    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     S    11_F     S    11_A      9   13   30      3    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     K    12_F     K    12_A      9   13   30      4    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     G    13_F     G    13_A      9   14   30      4    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     N    14_F     N    14_A      9   14   30      4    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     T    15_F     T    15_A      9   14   30      5    5    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     V    16_F     V    16_A      9   14   30      5    5    8   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     T    17_F     T    17_A      7   14   30      5    5    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     F    18_F     F    18_A      7   14   30      5    5    7   10   13   14   15   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     K    19_F     K    19_A      7   14   30      5    5    7    9   11   14   15   16   18   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     T    20_F     T    20_A      6   14   30      4    4    7   10   13   14   15   16   18   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     P    21_F     P    21_A      5   14   30      4    4    7   10   13   14   15   16   18   20   24   26   28   29   29   30   30   30   30   30 
LCS_GDT     D    22_F     D    22_A      5   14   30      4    4    7   10   13   14   15   16   18   22   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     E    23_F     E    23_A      5   14   30      3    4    7   10   13   14   15   16   18   22   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     S    24_F     S    24_A      4   14   30      3    4    7   10   13   14   15   16   18   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     S    25_F     S    25_A      4   14   30      3    8    9   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     I    26_F     I    26_A      4   14   30      3    3    6   11   13   14   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     A    27_F     A    27_A      4   14   30      3    3    4    9   11   13   16   20   21   22   23   24   28   28   29   30   30   30   30   30 
LCS_GDT     Y    28_F     Y    28_A      3    4   30      3    3    4    4    6    9   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     M    29_F     M    29_A      3    4   30      3    3    4    4   11   13   16   20   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_GDT     R    30_F     R    30_A      3    4   30      3    3    4    5   11   13   14   18   21   23   25   26   28   29   29   30   30   30   30   30 
LCS_AVERAGE  LCS_A:  12.70  (   4.78    9.11   24.19 )

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      5      8      9     11     13     14     16     20     21     23     25     26     28     29     29     30     30     30     30     30 
GDT PERCENT_AT   4.03   6.45   7.26   8.87  10.48  11.29  12.90  16.13  16.94  18.55  20.16  20.97  22.58  23.39  23.39  24.19  24.19  24.19  24.19  24.19
GDT RMS_LOCAL    0.31   0.59   0.71   1.08   1.48   1.75   2.16   2.85   2.92   3.67   4.05   4.12   4.36   4.57   4.52   4.71   4.71   4.71   4.71   4.71
GDT RMS_ALL_AT   9.56   5.89   5.93   6.02   5.99   6.08   7.06   6.14   6.20   5.01   4.76   4.77   4.79   4.72   4.73   4.71   4.71   4.71   4.71   4.71

# Checking swapping
#   possible swapping detected:  F     2_F      F     2_A
#   possible swapping detected:  Y    10_F      Y    10_A
#   possible swapping detected:  F    18_F      F    18_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_A    13.212     0    0.159   0.897    15.860    0.000    4.405
LGA    F     2_F      F     2_A    10.588     0    0.058   1.367    11.255    6.071    3.333
LGA    T     3_F      T     3_A     6.250     0    0.691   1.390     9.525   17.976   11.701
LGA    G     4_F      G     4_A     4.645     0    0.220   0.220     5.235   36.190   36.190
LGA    W     5_F      W     5_A     4.332     0    0.070   0.195    13.421   45.357   14.626
LGA    S     6_F      S     6_A     2.434     0    0.553   0.933     5.257   61.071   50.317
LGA    P     7_F      P     7_A     1.362     0    0.079   0.216     2.191   75.000   72.925
LGA    F     8_F      F     8_A     2.424     0    0.267   1.044     4.418   61.190   57.792
LGA    K     9_F      K     9_A     2.562     0    0.097   0.521     6.585   62.857   46.614
LGA    Y    10_F      Y    10_A     1.891     0    0.139   0.203     4.513   75.119   58.849
LGA    S    11_F      S    11_A     1.407     0    0.054   0.166     1.706   81.429   78.571
LGA    K    12_F      K    12_A     1.479     0    0.066   0.460     3.034   77.143   72.381
LGA    G    13_F      G    13_A     1.655     0    0.046   0.046     1.728   72.857   72.857
LGA    N    14_F      N    14_A     1.149     0    0.099   1.225     3.834   77.143   72.381
LGA    T    15_F      T    15_A     1.955     0    0.082   0.235     2.820   75.000   68.435
LGA    V    16_F      V    16_A     2.670     0    0.103   0.090     4.795   66.905   52.517
LGA    T    17_F      T    17_A     1.754     0    0.090   0.952     3.483   63.214   63.946
LGA    F    18_F      F    18_A     4.252     0    0.021   0.211     6.755   38.929   29.957
LGA    K    19_F      K    19_A     5.832     0    0.107   0.810     8.069   17.738   13.704
LGA    T    20_F      T    20_A     7.715     0    0.104   1.139     9.738    5.595    9.592
LGA    P    21_F      P    21_A    11.517     0    0.042   0.046    13.187    0.000    0.068
LGA    D    22_F      D    22_A    12.498     0    0.617   1.131    12.901    0.000    0.000
LGA    E    23_F      E    23_A    11.804     0    0.330   0.433    17.419    0.000    0.000
LGA    S    24_F      S    24_A    10.104     0    0.617   0.563    11.169    2.976    1.984
LGA    S    25_F      S    25_A     3.203     0    0.120   0.266     5.716   38.214   47.063
LGA    I    26_F      I    26_A     3.011     0    0.681   1.292     8.819   57.500   36.905
LGA    A    27_F      A    27_A     3.794     0    0.692   0.624     6.378   52.381   45.333
LGA    Y    28_F      Y    28_A     3.460     0    0.638   0.602     6.081   50.000   34.524
LGA    M    29_F      M    29_A     3.466     0    0.055   1.339     6.874   40.476   38.393
LGA    R    30_F      R    30_A     4.393     0    0.501   1.710    15.137   37.262   18.398

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     244    244  100.00               124
SUMMARY(RMSD_GDC):     4.710          4.661                  5.608           10.448    8.982

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   30  124    4.0     20    2.85    13.911    12.964     0.679

LGA_LOCAL      RMSD:   2.848  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.140  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:   4.710  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.941191 * X  +   0.033687 * Y  +   0.336190 * Z  + -75.847153
  Y_new =   0.332938 * X  +  -0.261929 * Y  +  -0.905840 * Z  + 121.797630
  Z_new =   0.057543 * X  +   0.964499 * Y  +  -0.257741 * Z  +  -2.418806 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.340004 -0.057575  1.831923   [DEG:   19.4808   -3.2988  104.9615 ]
ZXZ:  0.355379  1.831480  0.059590   [DEG:   20.3617  104.9361    3.4143 ]
 
# END of job
