
#######################################################
#                                                     #
#                        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   59 (  449),  selected   59 , name one
# Molecule2: number of CA atoms  243 ( 1787),  selected   59 , 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:    43     201_A - 243_A       4.96    10.95
  LONGEST_CONTINUOUS_SEGMENT:    43     202_A - 244_A       4.48    12.08
  LCS_AVERAGE:     15.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27     218_A - 244_A       1.83    16.88
  LCS_AVERAGE:      8.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17     228_A - 244_A       0.88    18.62
  LCS_AVERAGE:      5.57

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   59
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   186_A     D   186_A     11   14   21      8    8   11   14   14   15   15   15   18   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     A   187_A     A   187_A     11   14   21      8    9   11   14   14   15   15   15   16   16   17   18   20   36   45   49   52   53   55   57 
LCS_GDT     S   188_A     S   188_A     11   14   24      8    9   11   14   14   15   15   15   16   16   17   28   34   38   45   49   52   53   55   57 
LCS_GDT     A   189_A     A   189_A     11   14   26      8    9   11   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     I   190_A     I   190_A     11   14   26      8    9   11   14   14   15   15   16   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     V   191_A     V   191_A     11   14   26      8    9   11   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     A   192_A     A   192_A     11   14   26      8    9   11   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     L   193_A     L   193_A     11   14   26      8    9   10   14   14   15   15   16   20   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     H   194_A     H   194_A     11   14   26      3    9   10   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     T   195_A     T   195_A     11   14   26      4    9   11   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     D   196_A     D   196_A     11   14   26      4    7   11   14   14   15   15   15   16   22   25   29   34   38   44   49   52   53   55   57 
LCS_GDT     V   197_A     V   197_A      8   14   26      4    6   11   14   14   15   15   15   16   19   24   29   33   37   44   49   52   53   55   57 
LCS_GDT     M   198_A     M   198_A      5   14   28      4    4   11   14   14   15   15   16   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     R   199_A     R   199_A      7   14   29      5    5    8   14   14   15   15   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     P   200_A     P   200_A      7    8   31      5    5    7    7    9   10   13   14   16   22   25   30   34   38   45   49   52   53   55   57 
LCS_GDT     L   201_A     L   201_A      7    8   43      5    5    7    7    9    9   11   17   21   23   25   30   34   39   45   49   52   53   55   57 
LCS_GDT     A   202_A     A   202_A      7    8   43      5    5    7    9   11   15   16   17   21   23   29   34   38   40   45   49   52   53   55   57 
LCS_GDT     D   203_A     D   203_A      7    8   43      5    5    7    7    9   12   16   17   23   28   32   37   39   40   45   49   52   53   55   57 
LCS_GDT     A   204_A     A   204_A      7   17   43      4    5    8   11   15   16   17   17   22   27   31   35   39   40   45   49   52   53   55   57 
LCS_GDT     G   205_A     G   205_A     16   17   43      4   12   16   16   16   16   17   23   29   36   37   37   39   40   45   49   52   53   55   57 
LCS_GDT     P   206_A     P   206_A     16   17   43     10   14   16   16   16   24   30   34   35   37   38   39   39   40   40   41   44   49   54   57 
LCS_GDT     T   207_A     T   207_A     16   17   43     10   14   16   21   26   29   30   34   35   37   38   39   39   40   40   41   45   49   53   57 
LCS_GDT     L   208_A     L   208_A     16   17   43     12   14   16   16   16   16   21   28   34   36   37   39   39   40   45   49   52   53   55   57 
LCS_GDT     I   209_A     I   209_A     16   17   43     12   14   16   16   16   17   21   30   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     E   210_A     E   210_A     16   17   43     12   14   17   23   27   29   30   34   35   37   38   39   39   40   40   41   47   51   55   57 
LCS_GDT     T   211_A     T   211_A     16   17   43     12   14   16   19   26   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     L   212_A     L   212_A     16   17   43     12   14   16   16   16   17   30   33   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     D   213_A     D   213_A     16   17   43     12   14   16   16   19   26   29   34   35   37   38   39   39   40   41   48   52   53   55   57 
LCS_GDT     A   214_A     A   214_A     16   17   43     12   14   16   16   25   28   30   34   35   37   38   39   39   40   44   49   52   53   55   57 
LCS_GDT     Y   215_A     Y   215_A     16   17   43     12   14   18   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     L   216_A     L   216_A     16   17   43     12   14   16   16   16   26   29   34   35   37   38   39   39   40   44   49   52   53   55   57 
LCS_GDT     D   217_A     D   217_A     16   17   43     12   14   16   16   16   16   21   27   35   37   38   39   39   40   43   48   52   53   55   57 
LCS_GDT     C   218_A     C   218_A     16   27   43     12   14   16   16   16   16   21   29   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     G   219_A     G   219_A     16   27   43     12   14   17   23   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     G   220_A     G   220_A     16   27   43     10   14   16   18   26   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     A   221_A     A   221_A     11   27   43      6   11   19   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     I   222_A     I   222_A     11   27   43      7   11   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     E   223_A     E   223_A     11   27   43      7   11   19   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     A   224_A     A   224_A     11   27   43      7   11   18   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     C   225_A     C   225_A     11   27   43      7   11   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     A   226_A     A   226_A     11   27   43      7   11   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     R   227_A     R   227_A     11   27   43      7   11   18   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     K   228_A     K   228_A     17   27   43      7   11   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     L   229_A     L   229_A     17   27   43      6   11   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     F   230_A     F   230_A     17   27   43      4   13   20   24   27   29   30   34   35   37   38   39   39   40   43   48   51   53   55   57 
LCS_GDT     V   231_A     V   231_A     17   27   43      4   13   20   24   27   29   30   34   35   37   38   39   39   40   44   49   52   53   55   57 
LCS_GDT     H   232_A     H   232_A     17   27   43      4   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     P   233_A     P   233_A     17   27   43      4   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     N   234_A     N   234_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     T   235_A     T   235_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     V   236_A     V   236_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     R   237_A     R   237_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     Y   238_A     Y   238_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     R   239_A     R   239_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     L   240_A     L   240_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     K   241_A     K   241_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   45   49   52   53   55   57 
LCS_GDT     R   242_A     R   242_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   40   43   45   51   55   57 
LCS_GDT     I   243_A     I   243_A     17   27   43     10   13   20   24   27   29   30   34   35   37   38   39   39   40   40   40   42   43   43   44 
LCS_GDT     T   244_A     T   244_A     17   27   43      4   13   20   24   27   29   30   34   35   37   38   39   39   40   40   40   42   43   43   44 
LCS_AVERAGE  LCS_A:   9.93  (   5.57    8.34   15.90 )

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     14     20     24     27     29     30     34     35     37     38     39     39     40     45     49     52     53     55     57 
GDT PERCENT_AT   4.94   5.76   8.23   9.88  11.11  11.93  12.35  13.99  14.40  15.23  15.64  16.05  16.05  16.46  18.52  20.16  21.40  21.81  22.63  23.46
GDT RMS_LOCAL    0.32   0.44   1.01   1.24   1.47   1.64   1.74   2.25   2.34   2.63   2.79   2.98   2.98   3.25   5.57   5.84   6.08   6.14   6.36   6.55
GDT RMS_ALL_AT  19.23  19.07  18.18  17.53  16.77  16.51  16.58  15.81  15.66  15.32  15.40  15.08  15.08  14.47   7.03   7.06   7.00   7.00   6.93   6.91

# Checking swapping
#   possible swapping detected:  D   186_A      D   186_A
#   possible swapping detected:  D   196_A      D   196_A
#   possible swapping detected:  E   210_A      E   210_A
#   possible swapping detected:  D   213_A      D   213_A
#   possible swapping detected:  Y   215_A      Y   215_A
#   possible swapping detected:  E   223_A      E   223_A
#   possible swapping detected:  Y   238_A      Y   238_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D   186_A      D   186_A    31.257     0    0.233   1.383    33.077    0.000    0.000
LGA    A   187_A      A   187_A    30.185     0    0.033   0.033    31.301    0.000    0.000
LGA    S   188_A      S   188_A    34.367     0    0.049   0.675    37.427    0.000    0.000
LGA    A   189_A      A   189_A    33.003     0    0.023   0.035    33.476    0.000    0.000
LGA    I   190_A      I   190_A    27.854     0    0.022   0.615    29.564    0.000    0.000
LGA    V   191_A      V   191_A    30.302     0    0.046   0.048    33.272    0.000    0.000
LGA    A   192_A      A   192_A    33.202     0    0.106   0.124    34.723    0.000    0.000
LGA    L   193_A      L   193_A    29.310     0    0.072   1.398    31.412    0.000    0.000
LGA    H   194_A      H   194_A    25.205     0    0.143   0.285    26.552    0.000    0.000
LGA    T   195_A      T   195_A    29.640     0    0.038   1.079    33.080    0.000    0.000
LGA    D   196_A      D   196_A    31.883     0    0.174   1.084    37.349    0.000    0.000
LGA    V   197_A      V   197_A    27.555     0    0.102   0.126    29.125    0.000    0.000
LGA    M   198_A      M   198_A    24.235     0    0.598   1.316    25.575    0.000    0.000
LGA    R   199_A      R   199_A    25.917     0    0.580   1.471    33.554    0.000    0.000
LGA    P   200_A      P   200_A    25.542     0    0.066   0.262    30.060    0.000    0.000
LGA    L   201_A      L   201_A    22.196     0    0.093   1.383    24.292    0.000    0.000
LGA    A   202_A      A   202_A    17.728     0    0.129   0.183    19.847    0.000    0.000
LGA    D   203_A      D   203_A    15.648     0    0.237   1.351    18.828    0.000    0.000
LGA    A   204_A      A   204_A    14.528     0    0.151   0.150    16.197    0.000    0.000
LGA    G   205_A      G   205_A    10.331     0    0.532   0.532    11.955    2.976    2.976
LGA    P   206_A      P   206_A     4.766     0    0.184   0.368     6.405   38.929   34.490
LGA    T   207_A      T   207_A     3.971     0    0.038   0.064     7.342   38.810   30.408
LGA    L   208_A      L   208_A     7.353     0    0.088   0.166    12.824   15.357    7.738
LGA    I   209_A      I   209_A     6.222     0    0.016   0.129    10.384   27.143   15.595
LGA    E   210_A      E   210_A     1.685     0    0.016   0.747     6.342   73.333   50.370
LGA    T   211_A      T   211_A     3.357     0    0.046   1.081     7.912   57.262   41.293
LGA    L   212_A      L   212_A     4.427     0    0.050   0.132     9.925   45.119   26.250
LGA    D   213_A      D   213_A     4.378     0    0.097   0.699     6.391   41.905   32.321
LGA    A   214_A      A   214_A     3.514     0    0.042   0.038     4.220   50.238   47.619
LGA    Y   215_A      Y   215_A     1.672     0    0.053   1.329    13.925   86.190   35.238
LGA    L   216_A      L   216_A     3.912     0    0.049   0.125     8.409   41.429   26.905
LGA    D   217_A      D   217_A     6.741     0    0.054   0.292     9.868   15.952    9.643
LGA    C   218_A      C   218_A     5.576     0    0.049   0.166     7.829   30.476   24.365
LGA    G   219_A      G   219_A     2.332     0    0.032   0.032     3.214   76.310   76.310
LGA    G   220_A      G   220_A     2.894     0    0.587   0.587     2.894   69.048   69.048
LGA    A   221_A      A   221_A     0.639     0    0.227   0.288     1.888   88.214   85.143
LGA    I   222_A      I   222_A     0.881     0    0.031   0.617     3.026   90.476   79.881
LGA    E   223_A      E   223_A     1.196     0    0.039   1.070     6.689   83.690   56.825
LGA    A   224_A      A   224_A     1.211     0    0.046   0.054     1.476   83.690   83.238
LGA    C   225_A      C   225_A     0.445     0    0.090   0.342     1.276   97.619   93.730
LGA    A   226_A      A   226_A     1.426     0    0.070   0.085     1.963   79.405   78.095
LGA    R   227_A      R   227_A     1.733     0    0.122   0.759     4.019   72.976   66.277
LGA    K   228_A      K   228_A     1.071     0    0.057   1.311     6.804   81.429   62.540
LGA    L   229_A      L   229_A     1.218     0    0.110   0.246     2.214   81.429   79.345
LGA    F   230_A      F   230_A     0.920     0    0.305   0.487     3.005   83.810   71.948
LGA    V   231_A      V   231_A     1.583     0    0.191   0.245     2.420   79.286   73.061
LGA    H   232_A      H   232_A     0.926     0    0.032   0.129     2.549   85.952   75.762
LGA    P   233_A      P   233_A     1.965     0    0.069   0.097     2.382   70.952   69.456
LGA    N   234_A      N   234_A     2.454     0    0.089   0.186     4.623   68.810   53.869
LGA    T   235_A      T   235_A     1.378     0    0.058   0.108     2.093   83.810   79.184
LGA    V   236_A      V   236_A     0.819     0    0.061   0.117     1.444   90.476   86.599
LGA    R   237_A      R   237_A     1.325     0    0.043   1.508    10.211   83.690   45.195
LGA    Y   238_A      Y   238_A     1.463     0    0.054   0.193     4.681   81.429   60.913
LGA    R   239_A      R   239_A     1.529     0    0.021   1.775    10.969   77.143   42.511
LGA    L   240_A      L   240_A     1.294     0    0.076   1.429     5.738   83.690   65.298
LGA    K   241_A      K   241_A     0.477     0    0.087   0.458     2.980   88.333   77.407
LGA    R   242_A      R   242_A     2.171     0    0.049   0.967     2.883   64.881   68.615
LGA    I   243_A      I   243_A     2.721     0    0.082   0.669     4.577   55.595   53.214
LGA    T   244_A      T   244_A     2.761     0    0.610   0.547     3.191   59.167   60.476

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       59     236    236  100.00     449    449  100.00               243
SUMMARY(RMSD_GDC):     6.878          6.724                  7.909           10.808    9.050

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   59  243    4.0     34    2.25    12.449    11.551     1.445

LGA_LOCAL      RMSD:   2.252  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.809  Number of assigned atoms:   59 
Std_ASGN_ATOMS RMSD:   6.878  Standard rmsd on all 59 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.710115 * X  +   0.309128 * Y  +   0.632595 * Z  +  79.921654
  Y_new =  -0.111150 * X  +  -0.936415 * Y  +   0.332825 * Z  +  24.618832
  Z_new =   0.695257 * X  +   0.166031 * Y  +   0.699322 * Z  + -81.105492 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.986329 -0.768778  0.233102   [DEG: -171.1040  -44.0477   13.3557 ]
ZXZ:  2.055125  0.796348  1.336381   [DEG:  117.7500   45.6274   76.5690 ]
 
# END of job
