
#######################################################
#                                                     #
#                        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        4.70     7.14
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.64    12.17
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.54    12.73
  LCS_AVERAGE:     39.35

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    5   14   15   17   17   19   19   20   22   23   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   20      3    3    5    6    6   10   13   14   15   17   17   19   19   20   23   23   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      3    4   20      3    4    5    6    6    6    8   10   12   13   15   15   17   18   20   20   23   24   25   26 
LCS_GDT     L    11_D     L    11_F      3   12   20      3    4    5    6   10   11   13   14   15   17   17   19   19   20   23   23   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      7    8    9   11   11   11   13   14   15   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      7    8    9   11   11   11   13   14   15   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      7    8    9   11   11   11   13   14   15   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      7    8    9   11   11   11   13   14   15   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      7    8    9   11   11   12   14   15   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      7    8    9   11   11   11   13   14   15   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      7    8    9   11   11   11   13   14   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      7    8   10   13   13   13   14   15   16   17   17   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    7    9   11   11   11   13   14   15   17   17   19   20   20   22   23   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4    9   11   11   12   14   15   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     10   11   12   13   13   13   14   15   16   17   17   19   19   20   23   23   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     10   11   12   13   13   13   14   15   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     10   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     10   11   12   13   13   13   14   15   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     10   11   12   13   13   13   14   15   16   17   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     10   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     10   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     10   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     10   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     10   11   12   13   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      8   11   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    7   12   13   13   13   14   15   16   16   18   19   20   20   23   23   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.72  (  39.35   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     10     11     12     13     13     13     14     15     16     17     18     19     20     20     23     23     24     25     25     26 
GDT PERCENT_AT  38.46  42.31  46.15  50.00  50.00  50.00  53.85  57.69  61.54  65.38  69.23  73.08  76.92  76.92  88.46  88.46  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.30   0.35   0.54   0.97   0.97   0.97   1.70   2.19   2.64   3.70   3.99   4.19   4.40   4.21   5.16   5.16   5.46   5.67   5.67   5.91
GDT RMS_ALL_AT  12.68  12.70  12.73  11.72  11.72  11.72  11.53  10.36   9.61   8.75   6.70   6.76   6.83   7.32   6.23   6.23   5.97   5.95   5.95   5.91

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_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    26.561     0    0.291   0.917    28.887    0.000    0.000
LGA    Q     9_D      Q     9_F    20.473     0    0.594   0.763    22.948    0.000    0.000
LGA    K    10_D      K    10_F    20.800     0    0.038   0.746    27.847    0.000    0.000
LGA    L    11_D      L    11_F    17.325     0    0.615   0.637    18.693    0.000    0.000
LGA    N    12_D      N    12_F    13.854     0    0.571   0.974    15.133    0.119    0.060
LGA    S    13_D      S    13_F    12.864     0    0.042   0.741    15.898    0.000    0.000
LGA    W    14_D      W    14_F    14.928     0    0.059   0.447    22.992    0.000    0.000
LGA    D    15_D      D    15_F    10.459     0    0.050   0.111    15.360    6.071    3.036
LGA    V    16_D      V    16_F     4.623     0    0.044   0.108     6.809   27.024   28.231
LGA    F    17_D      F    17_F     9.231     0    0.025   1.179    17.648    5.714    2.078
LGA    G    18_D      G    18_F     6.876     0    0.132   0.132     7.681   26.905   26.905
LGA    N    19_D      N    19_F     1.543     0    0.267   1.120     6.942   54.643   43.333
LGA    W    20_D      W    20_F     6.259     0    0.098   1.265    15.882   20.595    6.224
LGA    F    21_D      F    21_F     4.312     0    0.579   1.058    10.999   47.262   21.905
LGA    D    22_D      D    22_F     2.891     0    0.565   1.149     9.273   61.071   36.488
LGA    L    23_D      L    23_F     2.185     0    0.108   0.528     2.568   68.810   68.869
LGA    A    24_D      A    24_F     1.793     0    0.054   0.068     1.979   75.000   74.571
LGA    S    25_D      S    25_F     1.796     0    0.138   0.542     2.575   79.405   74.603
LGA    W    26_D      W    26_F     1.376     0    0.015   0.778     4.901   83.810   65.578
LGA    I    27_D      I    27_F     0.489     0    0.033   0.048     0.813   97.619   96.429
LGA    K    28_D      K    28_F     0.479     0    0.066   0.594     3.174   97.619   85.450
LGA    Y    29_D      Y    29_F     0.292     0    0.000   0.232     0.594   97.619   97.619
LGA    I    30_D      I    30_F     0.893     0    0.079   0.740     3.097   85.952   78.690
LGA    Q    31_D      Q    31_F     1.650     0    0.073   0.964     8.131   75.000   50.899
LGA    R    32_D      R    32_F     1.387     0    0.481   1.144     6.369   77.262   61.558
LGA    R    33_D      R    33_F     1.558     0    0.581   0.904     5.349   79.405   52.597

# 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):     5.914          5.739                  7.512           44.881   37.505

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.19    59.615    55.342     0.654

LGA_LOCAL      RMSD:   2.194  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.361  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.914  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.957778 * X  +   0.140057 * Y  +  -0.251090 * Z  + -108.680527
  Y_new =   0.284381 * X  +  -0.589989 * Y  +   0.755672 * Z  + -130.319550
  Z_new =  -0.042303 * X  +  -0.795171 * Y  +  -0.604908 * Z  +   1.019445 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.288626  0.042315 -2.221128   [DEG:   16.5371    2.4245 -127.2612 ]
ZXZ: -2.820796  2.220447 -3.088443   [DEG: -161.6197  127.2222 -176.9548 ]
 
# END of job
