
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       2_B - 37_B        4.99     7.61
  LCS_AVERAGE:     86.79

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26       3_B - 28_B        1.96    11.82
  LCS_AVERAGE:     57.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       4_B - 24_B        0.99    13.06
  LCS_AVERAGE:     41.34

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      5   25   36      2    4    5   10   11   13   17   23   25   27   27   28   30   30   31   31   32   33   33   34 
LCS_GDT     S     3_B     S     3_B     11   26   36      6    8   10   19   20   23   26   27   27   28   29   30   30   31   33   33   34   35   35   35 
LCS_GDT     Q     4_B     Q     4_B     21   26   36      6   14   18   21   22   24   26   27   27   28   29   30   31   32   33   34   34   35   38   38 
LCS_GDT     R     5_B     R     5_B     21   26   36      6   13   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     L     6_B     L     6_B     21   26   36      6   13   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     F     7_B     F     7_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     V     8_B     V     8_B     21   26   36      6   11   17   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     L     9_B     L     9_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     D    10_B     D    10_B     21   26   36     10   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     N    11_B     N    11_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     E    12_B     E    12_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     R    13_B     R    13_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     Y    14_B     Y    14_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     D    15_B     D    15_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     S    16_B     S    16_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     F    17_B     F    17_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     I    18_B     I    18_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     T    19_B     T    19_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     Q    20_B     Q    20_B     21   26   36     12   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     L    21_B     L    21_B     21   26   36      4   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     E    22_B     E    22_B     21   26   36      8   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     A    23_B     A    23_B     21   26   36      4   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     P    24_B     P    24_B     21   26   36      6   16   19   21   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     V    25_B     V    25_B     20   26   36      5    9   17   20   22   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     Q    26_B     Q    26_B     14   26   36      5    7   14   19   21   23   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     N    27_B     N    27_B     14   26   36      5    8   14   17   21   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     A    28_B     A    28_B     14   26   36      5   11   14   18   21   24   26   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     E    29_B     E    29_B     14   25   36      5   11   14   16   18   22   25   27   27   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     G    30_B     G    30_B     14   20   36      8   11   14   16   18   20   21   22   26   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     R    31_B     R    31_B     14   20   36      8   11   14   16   18   20   21   25   26   28   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     E    32_B     E    32_B     14   20   36      8   11   14   16   18   20   21   22   25   27   29   31   31   32   33   34   35   37   38   38 
LCS_GDT     R    33_B     R    33_B     14   20   36      8   11   14   16   18   20   21   21   22   25   28   31   31   32   33   34   35   37   38   38 
LCS_GDT     L    34_B     L    34_B     14   20   36      8   11   14   16   18   20   21   21   22   25   28   31   31   32   33   34   35   37   38   38 
LCS_GDT     M    35_B     M    35_B     14   20   36      8   11   14   16   18   20   21   21   22   25   28   31   31   32   33   34   35   37   38   38 
LCS_GDT     A    36_B     A    36_B     14   20   36      8   11   14   16   18   20   21   21   22   23   26   29   31   32   33   34   35   37   38   38 
LCS_GDT     V    37_B     V    37_B     14   20   36      8   11   14   16   18   20   21   21   22   23   25   26   30   31   33   34   35   37   38   38 
LCS_GDT     K    38_B     K    38_B     14   20   35      6   11   14   16   18   20   21   21   22   23   24   26   27   29   32   34   35   37   38   38 
LCS_GDT     P    39_B     P    39_B     14   20   35      3   10   14   16   18   20   21   21   22   23   24   26   27   28   31   33   35   37   38   38 
LCS_GDT     E    40_B     E    40_B     14   20   31      3    8   14   16   18   19   21   21   21   22   24   24   25   25   28   29   30   32   34   37 
LCS_GDT     W    41_B     W    41_B      5   20   31      3    3   11   15   16   20   21   21   22   23   24   26   27   28   32   34   35   37   38   38 
LCS_GDT     K    42_B     K    42_B      3    3   31      3    3    3    3    4    4    4    7    8   13   15   21   24   27   30   32   34   37   38   38 
LCS_AVERAGE  LCS_A:  61.93  (  41.34   57.64   86.79 )

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     12     16     19     21     22     24     26     27     27     28     29     31     31     32     33     34     35     37     38     38 
GDT PERCENT_AT  29.27  39.02  46.34  51.22  53.66  58.54  63.41  65.85  65.85  68.29  70.73  75.61  75.61  78.05  80.49  82.93  85.37  90.24  92.68  92.68
GDT RMS_LOCAL    0.30   0.54   0.80   0.99   1.14   1.71   1.96   2.21   2.21   2.60   2.77   3.74   3.74   3.85   4.07   4.43   4.94   5.30   5.51   5.51
GDT RMS_ALL_AT  13.42  13.32  12.82  13.06  12.64  11.24  11.82  11.19  11.19   9.73  10.21   7.58   7.58   7.75   8.08   7.08   6.89   6.93   6.76   6.76

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  D    10_B      D    10_B
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     6.870     0    0.379   0.524     7.970   13.452   12.190
LGA    S     3_B      S     3_B     4.300     0    0.308   0.373     5.583   51.786   42.460
LGA    Q     4_B      Q     4_B     1.673     0    0.051   0.797     4.522   65.000   54.762
LGA    R     5_B      R     5_B     2.929     0    0.109   1.589     9.400   59.762   34.199
LGA    L     6_B      L     6_B     2.566     0    0.148   0.193     5.212   69.048   53.274
LGA    F     7_B      F     7_B     1.020     0    0.041   0.176     4.741   72.976   56.450
LGA    V     8_B      V     8_B     2.613     0    0.049   1.173     5.688   64.881   55.578
LGA    L     9_B      L     9_B     1.186     0    0.036   0.202     1.908   75.000   80.476
LGA    D    10_B      D    10_B     1.957     0    0.061   1.144     2.472   79.405   75.179
LGA    N    11_B      N    11_B     1.538     0    0.084   1.262     4.825   77.143   64.881
LGA    E    12_B      E    12_B     1.566     0    0.055   1.103     6.937   77.143   57.143
LGA    R    13_B      R    13_B     0.982     0    0.028   1.229     4.565   88.214   75.758
LGA    Y    14_B      Y    14_B     0.182     0    0.043   0.186     0.589  100.000   98.413
LGA    D    15_B      D    15_B     0.535     0    0.042   0.453     1.603   92.857   88.333
LGA    S    16_B      S    16_B     1.009     0    0.094   0.658     3.171   85.952   79.206
LGA    F    17_B      F    17_B     1.023     0    0.065   0.328     1.719   88.214   80.000
LGA    I    18_B      I    18_B     0.793     0    0.029   0.644     2.206   90.476   87.262
LGA    T    19_B      T    19_B     1.013     0    0.042   1.171     3.079   83.690   74.762
LGA    Q    20_B      Q    20_B     1.828     0    0.034   1.058     3.504   72.857   64.339
LGA    L    21_B      L    21_B     1.787     0    0.079   0.798     2.357   77.143   76.250
LGA    E    22_B      E    22_B     0.872     0    0.545   0.915     1.859   86.190   84.603
LGA    A    23_B      A    23_B     1.783     0    0.056   0.085     2.078   70.833   69.619
LGA    P    24_B      P    24_B     1.510     0    0.085   0.273     1.800   77.143   76.531
LGA    V    25_B      V    25_B     1.480     0    0.122   0.278     2.472   73.095   75.442
LGA    Q    26_B      Q    26_B     3.131     0    0.083   1.186     9.969   57.262   32.751
LGA    N    27_B      N    27_B     3.460     0    0.049   1.374     8.913   46.786   28.274
LGA    A    28_B      A    28_B     2.998     0    0.058   0.058     5.706   45.119   46.095
LGA    E    29_B      E    29_B     5.161     0    0.126   1.150     7.897   23.452   27.566
LGA    G    30_B      G    30_B     7.642     0    0.117   0.117     9.108    8.214    8.214
LGA    R    31_B      R    31_B     7.280     0    0.044   1.034    10.180    6.548   12.727
LGA    E    32_B      E    32_B    10.338     0    0.064   1.145    13.023    0.714    0.370
LGA    R    33_B      R    33_B    12.703     0    0.044   1.159    15.294    0.000    0.000
LGA    L    34_B      L    34_B    13.343     0    0.025   0.917    15.656    0.000    0.000
LGA    M    35_B      M    35_B    14.683     0    0.108   0.288    17.811    0.000    0.000
LGA    A    36_B      A    36_B    17.335     0    0.162   0.161    19.707    0.000    0.000
LGA    V    37_B      V    37_B    19.769     0    0.063   1.065    20.928    0.000    0.000
LGA    K    38_B      K    38_B    23.708     4    0.152   0.171    25.723    0.000    0.000
LGA    P    39_B      P    39_B    24.289     0    0.065   0.340    27.627    0.000    0.000
LGA    E    40_B      E    40_B    29.838     0    0.481   1.354    33.540    0.000    0.000
LGA    W    41_B      W    41_B    27.518     0    0.057   1.090    28.248    0.000    0.000
LGA    K    42_B      K    42_B    26.332     0    0.482   0.969    26.648    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     6.581          6.484                  6.841           48.301   43.247

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     27    2.21    59.756    60.282     1.169

LGA_LOCAL      RMSD:   2.209  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.193  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   6.581  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.840988 * X  +  -0.428031 * Y  +   0.330952 * Z  +   6.961961
  Y_new =  -0.035154 * X  +   0.653615 * Y  +   0.756010 * Z  + -36.998486
  Z_new =  -0.539911 * X  +   0.624161 * Y  +  -0.564729 * Z  +  82.335419 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.099816  0.570332  2.306247   [DEG: -177.6064   32.6776  132.1382 ]
ZXZ:  2.728963  2.170901 -0.713149   [DEG:  156.3580  124.3835  -40.8604 ]
 
# END of job
