
#######################################################
#                                                     #
#                        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   55 (  455),  selected   55 , name one
# Molecule2: number of CA atoms  318 ( 2589),  selected   55 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40     209_A - 248_A       4.87    12.51
  LCS_AVERAGE:     12.15

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23     212_A - 234_A       1.71    14.95
  LCS_AVERAGE:      6.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     214_A - 233_A       0.94    15.81
  LCS_AVERAGE:      4.63

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   55
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     D   194_A     D   194_A      3    4   35      0    3    3    3    4    5    5    6    9   12   22   25   32   34   37   40   43   44   46   47 
LCS_GDT     E   195_A     E   195_A      9   21   35      5    6   11   14   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     N   196_A     N   196_A     10   21   35      5    7   11   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     L   197_A     L   197_A     11   21   35      5    8   12   16   19   21   22   24   24   26   28   29   32   34   36   40   43   44   46   47 
LCS_GDT     A   198_A     A   198_A     14   21   35      5    9   15   16   19   21   22   24   24   26   28   29   32   34   36   40   43   43   46   47 
LCS_GDT     E   199_A     E   199_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     Q   200_A     Q   200_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     A   201_A     A   201_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     F   202_A     F   202_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     L   203_A     L   203_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     S   204_A     S   204_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     Y   205_A     Y   205_A     14   21   35      7    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     S   206_A     S   206_A     14   21   35      3    8   15   16   19   21   22   24   24   26   29   31   32   34   37   40   43   44   46   47 
LCS_GDT     W   207_A     W   207_A     14   21   35      4    9   15   16   19   21   22   24   24   26   28   29   32   34   37   40   43   44   46   47 
LCS_GDT     W   208_A     W   208_A     14   21   35      3    8   15   16   19   21   22   24   25   26   30   31   32   35   37   40   43   44   46   47 
LCS_GDT     L   209_A     L   209_A     14   21   40      4    8   15   16   19   21   23   24   26   29   30   33   34   35   37   40   43   44   46   47 
LCS_GDT     L   210_A     L   210_A     14   21   40      4    8   15   16   19   21   22   24   25   26   27   29   31   33   35   38   39   43   45   47 
LCS_GDT     N   211_A     N   211_A     14   21   40      3    8   15   16   19   21   22   24   24   26   27   28   29   31   36   39   43   44   46   47 
LCS_GDT     K   212_A     K   212_A      7   23   40      3    6   10   16   20   21   23   24   26   29   30   33   34   35   37   40   43   44   46   47 
LCS_GDT     G   213_A     G   213_A      7   23   40      3    8   15   17   20   21   23   24   26   29   31   33   34   36   37   40   43   44   46   47 
LCS_GDT     W   214_A     W   214_A     20   23   40      9   16   20   20   20   21   23   24   27   29   31   33   35   36   36   40   43   44   46   47 
LCS_GDT     I   215_A     I   215_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     D   216_A     D   216_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     I   217_A     I   217_A     20   23   40     10   16   20   20   20   21   22   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     K   218_A     K   218_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     N   219_A     N   219_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     Q   220_A     Q   220_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     V   221_A     V   221_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     E   222_A     E   222_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     S   223_A     S   223_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     S   224_A     S   224_A     20   23   40     10   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     V   225_A     V   225_A     20   23   40      9   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     E   226_A     E   226_A     20   23   40      5   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     D   227_A     D   227_A     20   23   40      8   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     I   228_A     I   228_A     20   23   40      8   16   20   20   20   21   23   24   26   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     F   229_A     F   229_A     20   23   40      8   14   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     G   230_A     G   230_A     20   23   40      8   16   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     D   231_A     D   231_A     20   23   40      8   14   20   20   20   21   23   24   27   29   31   33   35   36   36   38   42   44   46   47 
LCS_GDT     I   232_A     I   232_A     20   23   40      8   14   20   20   20   21   23   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     N   233_A     N   233_A     20   23   40      4   14   20   20   20   21   23   24   27   29   31   33   35   36   36   38   42   44   46   47 
LCS_GDT     P   234_A     P   234_A     15   23   40      4    4    6   11   17   21   22   23   25   26   29   32   35   36   36   38   42   44   46   47 
LCS_GDT     R   235_A     R   235_A      4   14   40      4    4    4    6    6    7   10   16   17   20   24   30   35   36   36   38   38   40   41   43 
LCS_GDT     Q   236_A     Q   236_A      4   14   40      4    4   10   13   13   18   21   24   27   29   31   33   35   36   36   38   38   40   42   44 
LCS_GDT     E   237_A     E   237_A     12   14   40      3    8   12   12   13   18   22   24   27   29   31   33   35   36   36   38   38   40   42   46 
LCS_GDT     L   238_A     L   238_A     12   14   40      6   10   12   13   13   18   21   24   27   29   31   33   35   36   36   38   38   40   42   46 
LCS_GDT     S   239_A     S   239_A     12   14   40      6   10   12   13   13   14   19   22   24   27   29   32   35   36   36   38   38   40   41   43 
LCS_GDT     I   240_A     I   240_A     12   14   40      6   10   12   13   13   16   19   22   24   27   30   32   35   36   36   38   38   40   41   43 
LCS_GDT     E   241_A     E   241_A     12   14   40      6   10   12   13   13   17   19   22   24   27   30   32   35   36   36   38   38   40   42   46 
LCS_GDT     E   242_A     E   242_A     12   14   40      6   10   12   13   13   18   20   23   27   29   31   33   35   36   36   38   39   43   45   47 
LCS_GDT     F   243_A     F   243_A     12   14   40      6   10   12   13   13   19   22   24   27   29   31   33   35   36   36   39   43   44   46   47 
LCS_GDT     A   244_A     A   244_A     12   14   40      5   10   12   13   13   19   22   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     T   245_A     T   245_A     12   14   40      5   10   12   13   13   14   16   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     L   246_A     L   246_A     12   14   40      5   10   12   13   13   14   16   19   26   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     I   247_A     I   247_A     12   14   40      3   10   12   13   13   19   23   24   26   29   31   33   35   36   37   40   43   44   46   47 
LCS_GDT     N   248_A     N   248_A     12   14   40      3   10   12   13   13   14   16   24   27   29   31   33   35   36   37   40   43   44   46   47 
LCS_AVERAGE  LCS_A:   7.66  (   4.63    6.21   12.15 )

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     16     20     20     20     21     23     24     27     29     31     33     35     36     37     40     43     44     46     47 
GDT PERCENT_AT   3.14   5.03   6.29   6.29   6.29   6.60   7.23   7.55   8.49   9.12   9.75  10.38  11.01  11.32  11.64  12.58  13.52  13.84  14.47  14.78
GDT RMS_LOCAL    0.27   0.81   0.94   0.94   0.94   1.13   2.10   2.13   2.94   3.10   3.30   3.65   3.91   4.03   5.10   5.30   5.60   5.83   6.02   6.13
GDT RMS_ALL_AT  16.03  15.94  15.81  15.81  15.81  15.98  13.04  13.19  14.06  14.08  13.55  12.59  14.59  13.94   7.93   8.16   8.09   7.84   7.80   7.81

# Checking swapping
#   possible swapping detected:  E   195_A      E   195_A
#   possible swapping detected:  E   199_A      E   199_A
#   possible swapping detected:  F   202_A      F   202_A
#   possible swapping detected:  E   222_A      E   222_A
#   possible swapping detected:  E   237_A      E   237_A
#   possible swapping detected:  E   241_A      E   241_A
#   possible swapping detected:  F   243_A      F   243_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D   194_A      D   194_A    26.513     0    0.628   0.661    27.943    0.000    0.000
LGA    E   195_A      E   195_A    30.359     0    0.572   0.950    36.941    0.000    0.000
LGA    N   196_A      N   196_A    29.265     0    0.039   1.396    29.867    0.000    0.000
LGA    L   197_A      L   197_A    29.798     0    0.060   0.164    32.760    0.000    0.000
LGA    A   198_A      A   198_A    28.734     0    0.216   0.214    29.653    0.000    0.000
LGA    E   199_A      E   199_A    25.864     0    0.021   0.891    28.728    0.000    0.000
LGA    Q   200_A      Q   200_A    24.776     0    0.046   0.834    28.132    0.000    0.000
LGA    A   201_A      A   201_A    23.127     0    0.089   0.103    24.317    0.000    0.000
LGA    F   202_A      F   202_A    20.895     0    0.041   0.105    22.004    0.000    0.000
LGA    L   203_A      L   203_A    19.019     0    0.053   0.200    21.497    0.000    0.000
LGA    S   204_A      S   204_A    18.329     0    0.079   0.650    19.904    0.000    0.000
LGA    Y   205_A      Y   205_A    15.054     0    0.034   0.496    20.668    0.000    0.000
LGA    S   206_A      S   206_A    11.798     0    0.016   0.168    13.449    0.357    0.238
LGA    W   207_A      W   207_A    10.613     0    0.173   1.184    15.156    2.500    0.714
LGA    W   208_A      W   208_A     7.293     0    0.109   0.106     8.688   16.429   13.333
LGA    L   209_A      L   209_A     4.428     0    0.069   1.415     7.109   36.429   32.738
LGA    L   210_A      L   210_A     5.797     0    0.104   0.159     8.865   18.690   14.345
LGA    N   211_A      N   211_A     7.306     0    0.284   0.342    11.768   12.619    6.548
LGA    K   212_A      K   212_A     3.696     0    0.283   1.326    11.941   55.238   29.683
LGA    G   213_A      G   213_A     2.395     0    0.063   0.063     2.685   67.024   67.024
LGA    W   214_A      W   214_A     1.784     0    0.291   1.181    12.723   79.643   32.279
LGA    I   215_A      I   215_A     0.915     0    0.033   1.311     3.913   88.214   77.083
LGA    D   216_A      D   216_A     1.681     0    0.000   0.341     3.244   75.000   65.238
LGA    I   217_A      I   217_A     2.573     0    0.051   0.642     3.650   62.857   54.762
LGA    K   218_A      K   218_A     2.106     0    0.047   0.808     7.363   68.810   48.307
LGA    N   219_A      N   219_A     0.633     0    0.063   0.113     2.269   90.476   80.714
LGA    Q   220_A      Q   220_A     1.475     0    0.043   1.393     6.064   77.143   57.884
LGA    V   221_A      V   221_A     2.211     0    0.032   0.076     3.252   68.810   61.769
LGA    E   222_A      E   222_A     1.600     0    0.050   0.579     4.566   77.143   63.545
LGA    S   223_A      S   223_A     0.410     0    0.000   0.581     1.415   92.857   90.556
LGA    S   224_A      S   224_A     1.404     0    0.042   0.127     1.822   79.286   77.143
LGA    V   225_A      V   225_A     1.644     0    0.037   0.124     2.615   77.143   70.748
LGA    E   226_A      E   226_A     0.898     0    0.047   0.924     4.241   88.214   73.175
LGA    D   227_A      D   227_A     1.645     0    0.095   0.966     2.565   77.262   75.357
LGA    I   228_A      I   228_A     1.532     0    0.070   0.645     2.008   77.143   75.060
LGA    F   229_A      F   229_A     0.645     0    0.198   0.305     3.425   90.595   74.589
LGA    G   230_A      G   230_A     0.815     0    0.051   0.051     1.513   83.810   83.810
LGA    D   231_A      D   231_A     1.549     0    0.073   0.172     3.124   77.143   68.214
LGA    I   232_A      I   232_A     0.798     0    0.182   0.764     2.867   85.952   84.048
LGA    N   233_A      N   233_A     2.823     0    0.498   1.219     4.883   52.262   45.655
LGA    P   234_A      P   234_A     4.432     0    0.101   0.333     6.249   30.833   27.007
LGA    R   235_A      R   235_A     9.521     0    0.025   0.998    20.700    2.024    0.736
LGA    Q   236_A      Q   236_A     9.462     0    0.596   1.286    15.147    2.262    1.164
LGA    E   237_A      E   237_A     8.855     0    0.658   0.922    11.199    1.071    2.222
LGA    L   238_A      L   238_A    11.002     0    0.069   0.153    13.034    0.000    3.929
LGA    S   239_A      S   239_A    15.517     0    0.043   0.087    17.716    0.000    0.000
LGA    I   240_A      I   240_A    14.408     0    0.063   1.001    15.852    0.000    0.000
LGA    E   241_A      E   241_A    16.025     0    0.030   0.376    21.932    0.000    0.000
LGA    E   242_A      E   242_A    13.388     0    0.098   1.049    17.078    0.000    0.000
LGA    F   243_A      F   243_A     8.022     0    0.066   1.229    10.119    7.262   16.147
LGA    A   244_A      A   244_A     8.734     0    0.052   0.053    10.393    2.500    2.000
LGA    T   245_A      T   245_A    11.607     0    0.185   1.095    16.363    0.000    0.000
LGA    L   246_A      L   246_A     8.636     0    0.033   1.414     9.289    5.357    6.845
LGA    I   247_A      I   247_A     4.388     0    0.071   0.705     6.267   24.286   55.179
LGA    N   248_A      N   248_A     8.151     0    0.570   1.596    11.702    4.524    2.560

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       55     220    220  100.00     455    455  100.00               318
SUMMARY(RMSD_GDC):     7.440          7.283                  8.409            5.846    5.165

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   55  318    4.0     24    2.13     7.862     7.522     1.076

LGA_LOCAL      RMSD:   2.131  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.194  Number of assigned atoms:   55 
Std_ASGN_ATOMS RMSD:   7.440  Standard rmsd on all 55 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.245283 * X  +   0.281067 * Y  +   0.927813 * Z  + -155.389465
  Y_new =   0.726613 * X  +  -0.580261 * Y  +   0.367873 * Z  + -134.016983
  Z_new =   0.641771 * X  +   0.764394 * Y  +  -0.061899 * Z  + -184.568573 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.896355 -0.696805  1.651597   [DEG:  108.6531  -39.9240   94.6296 ]
ZXZ:  1.948277  1.632735  0.698414   [DEG:  111.6281   93.5488   40.0162 ]
 
# END of job
