
#######################################################
#                                                     #
#                        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   50 (  396),  selected   50 , name one
# Molecule2: number of CA atoms  594 ( 4909),  selected   50 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39     235_B - 273_B       4.85     8.17
  LCS_AVERAGE:      6.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18     238_B - 255_B       1.94    10.71
  LCS_AVERAGE:      2.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15     239_B - 253_B       0.67    11.29
  LCS_AVERAGE:      1.63

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   50
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   224_A     A   224_B      6    8   17      4    6    6    7    8   11   12   13   13   14   15   15   16   18   21   25   29   32   33   33 
LCS_GDT     Y   225_A     Y   225_B      6    8   17      5    6    6    7    8   11   12   13   13   14   15   15   16   18   25   28   29   32   33   33 
LCS_GDT     K   226_A     K   226_B      6    8   17      5    6    6    7    8   11   12   13   14   19   22   24   24   27   29   35   38   41   44   46 
LCS_GDT     L   227_A     L   227_B      6    8   28      5    6    6    7    8   11   12   13   14   19   22   24   24   27   29   30   38   41   44   46 
LCS_GDT     F   228_A     F   228_B      6    8   28      5    6    6    7    8   11   12   18   22   25   28   31   34   36   37   40   40   44   45   46 
LCS_GDT     T   229_A     T   229_B      6    8   28      5    6    6    7    8   11   13   19   22   25   29   31   34   36   38   40   40   44   45   46 
LCS_GDT     V   230_A     V   230_B      3    8   28      3    3    5    9   11   14   17   21   27   30   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   231_A     L   231_B      3    8   28      2    3    8   12   13   16   17   24   28   30   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     N   232_A     N   232_B      4    7   28      3    4   12   12   14   16   17   18   19   21   27   32   37   37   38   40   42   44   45   46 
LCS_GDT     D   233_A     D   233_B      4    7   30      7    9   12   12   14   16   17   18   19   21   25   29   37   37   38   40   42   44   45   46 
LCS_GDT     R   234_A     R   234_B      4    7   30      3    4    4    6    7   15   15   18   19   20   25   29   37   37   38   40   42   44   45   46 
LCS_GDT     G   235_A     G   235_B      4    7   39      3    4    5    6    7   10   12   13   19   19   22   29   31   33   38   40   41   43   45   46 
LCS_GDT     I   236_A     I   236_B      4    7   39      3    4    5    6   11   14   17   20   28   30   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     N   237_A     N   237_B      4    7   39      3    4    5    7   10   12   17   24   28   31   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   238_A     L   238_B      4   18   39      2    4    5    9   13   17   22   27   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     T   239_A     T   239_B     15   18   39      7   12   15   15   15   18   26   29   31   33   33   34   35   36   38   40   41   44   45   46 
LCS_GDT     E   240_A     E   240_B     15   18   39      7   13   15   15   15   18   26   29   31   33   33   34   35   36   38   40   42   44   45   46 
LCS_GDT     G   241_A     G   241_B     15   18   39      9   13   15   15   15   17   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     E   242_A     E   242_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   243_A     L   243_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   244_A     L   244_B     15   18   39      7   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     K   245_A     K   245_B     15   18   39      7   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     A   246_A     A   246_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     H   247_A     H   247_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     T   248_A     T   248_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     I   249_A     I   249_B     15   18   39      9   13   15   15   15   17   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     G   250_A     G   250_B     15   18   39      9   13   15   15   15   16   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     I   251_A     I   251_B     15   18   39      9   13   15   15   15   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     C   252_A     C   252_B     15   18   39      9   13   15   15   15   16   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     S   253_A     S   253_B     15   18   39      7   13   15   15   15   16   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     D   254_A     D   254_B      5   18   39      3    4    5    7   14   16   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     N   255_A     N   255_B      5   18   39      4    4    5    9   14   17   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   256_A     L   256_B      5    8   39      4    4    5    6    8   12   15   22   30   32   33   34   35   36   38   40   42   44   45   46 
LCS_GDT     S   257_A     S   257_B      6    8   39      5    5    6    9   14   16   24   29   30   33   33   34   35   36   38   40   42   44   45   46 
LCS_GDT     H   258_A     H   258_B      6    8   39      5    5   10   10   13   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     Q   259_A     Q   259_B      6    8   39      5    5    6    7    7    8   16   16   18   21   24   27   34   36   36   37   42   44   45   46 
LCS_GDT     R   260_A     R   260_B      6    7   39      5    5    6    7   10   10   15   16   20   26   30   33   35   36   36   37   42   43   45   45 
LCS_GDT     T   261_A     T   261_B      6   13   39      5    5    6    7   11   17   25   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     I   262_A     I   262_B     12   13   39     10   10   12   12   14   16   17   26   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     S   263_A     S   263_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     D   264_A     D   264_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     N   265_A     N   265_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     W   266_A     W   266_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     D   267_A     D   267_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     A   268_A     A   268_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     I   269_A     I   269_B     12   13   39     10   10   12   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     L   270_A     L   270_B     12   13   39     10   10   12   12   14   17   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     K   271_A     K   271_B     12   13   39     10   10   12   12   14   16   19   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     H   272_A     H   272_B     12   13   39      3    7   11   12   14   18   26   29   31   33   33   34   37   37   38   40   42   44   45   46 
LCS_GDT     P   273_A     P   273_B     12   13   39      3    3    3   12   14   16   17   24   29   33   33   34   37   37   38   40   42   44   45   46 
LCS_AVERAGE  LCS_A:   3.28  (   1.63    2.15    6.06 )

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     13     15     15     15     18     26     29     31     33     33     34     37     37     38     40     42     44     45     46 
GDT PERCENT_AT   1.68   2.19   2.53   2.53   2.53   3.03   4.38   4.88   5.22   5.56   5.56   5.72   6.23   6.23   6.40   6.73   7.07   7.41   7.58   7.74
GDT RMS_LOCAL    0.33   0.51   0.67   0.67   0.67   2.34   2.70   2.84   3.02   3.23   3.23   3.36   4.28   4.28   4.33   4.68   5.15   5.36   5.50   5.78
GDT RMS_ALL_AT   9.18  11.16  11.29  11.29  11.29   9.51   9.56   9.69   9.22   9.28   9.28   9.43   7.52   7.52   7.61   7.29   7.47   7.19   7.21   7.08

# Checking swapping
#   possible swapping detected:  Y   225_A      Y   225_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A   224_A      A   224_B    23.675     0    0.082   0.082    25.050    0.000    0.000
LGA    Y   225_A      Y   225_B    21.155     0    0.045   0.107    22.405    0.000    0.000
LGA    K   226_A      K   226_B    21.025     0    0.104   0.986    24.357    0.000    0.000
LGA    L   227_A      L   227_B    19.692     0    0.154   0.334    24.019    0.000    0.000
LGA    F   228_A      F   228_B    14.835     0    0.285   1.542    17.223    0.000    0.000
LGA    T   229_A      T   229_B    14.311     0    0.163   0.970    17.416    0.000    0.000
LGA    V   230_A      V   230_B    14.025     0    0.030   1.073    17.499    0.000    0.000
LGA    L   231_A      L   231_B    14.466     0    0.296   1.222    16.433    0.000    0.000
LGA    N   232_A      N   232_B    17.760     0    0.624   1.366    23.862    0.000    0.000
LGA    D   233_A      D   233_B    15.860     0    0.321   0.983    17.713    0.000    0.000
LGA    R   234_A      R   234_B    17.842     0    0.693   1.294    29.151    0.000    0.000
LGA    G   235_A      G   235_B    18.135     0    0.275   0.275    18.377    0.000    0.000
LGA    I   236_A      I   236_B    12.513     0    0.135   1.483    14.623    0.000    0.000
LGA    N   237_A      N   237_B    10.390     0    0.692   0.581    12.574    0.833    0.417
LGA    L   238_A      L   238_B     5.741     0    0.624   0.534    11.103   33.690   18.571
LGA    T   239_A      T   239_B     2.396     0    0.606   0.793     6.995   62.857   44.626
LGA    E   240_A      E   240_B     2.784     0    0.089   1.544     6.642   59.048   47.460
LGA    G   241_A      G   241_B     2.940     0    0.154   0.154     2.940   60.952   60.952
LGA    E   242_A      E   242_B     2.171     0    0.028   0.825     3.218   70.952   67.672
LGA    L   243_A      L   243_B     0.814     0    0.055   0.072     1.974   90.595   84.940
LGA    L   244_A      L   244_B     1.681     0    0.055   1.423     2.962   72.857   72.083
LGA    K   245_A      K   245_B     2.194     0    0.077   0.965    11.017   66.786   38.889
LGA    A   246_A      A   246_B     2.297     0    0.026   0.025     2.541   62.857   63.238
LGA    H   247_A      H   247_B     1.556     0    0.077   1.363     6.633   71.071   52.524
LGA    T   248_A      T   248_B     1.876     0    0.030   0.969     3.064   66.905   66.190
LGA    I   249_A      I   249_B     3.228     0    0.031   0.665     4.563   50.119   44.524
LGA    G   250_A      G   250_B     3.573     0    0.062   0.062     4.166   43.452   43.452
LGA    I   251_A      I   251_B     3.008     0    0.030   0.142     3.407   50.000   56.488
LGA    C   252_A      C   252_B     3.400     0    0.371   0.345     3.863   53.690   50.238
LGA    S   253_A      S   253_B     3.873     0    0.112   0.139     6.219   52.619   42.302
LGA    D   254_A      D   254_B     3.261     0    0.096   0.447     5.342   48.333   37.917
LGA    N   255_A      N   255_B     3.306     0    0.263   0.988     5.061   55.476   50.774
LGA    L   256_A      L   256_B     6.709     0    0.033   1.402    13.350   16.667    8.512
LGA    S   257_A      S   257_B     5.282     0    0.285   0.408     5.679   32.024   30.079
LGA    H   258_A      H   258_B     3.187     0    0.049   1.263     9.033   42.500   25.333
LGA    Q   259_A      Q   259_B     8.518     0    0.061   1.068    15.215    6.310    2.804
LGA    R   260_A      R   260_B     8.573     0    0.140   1.132    17.124    7.619    2.814
LGA    T   261_A      T   261_B     3.648     0    0.543   1.217     5.875   39.048   38.707
LGA    I   262_A      I   262_B     4.706     0    0.544   0.681    10.982   42.024   23.214
LGA    S   263_A      S   263_B     2.838     0    0.065   0.678     4.283   59.167   55.159
LGA    D   264_A      D   264_B     2.125     0    0.065   0.077     3.329   66.786   61.071
LGA    N   265_A      N   265_B     2.914     0    0.058   0.143     5.810   60.952   46.429
LGA    W   266_A      W   266_B     3.047     0    0.066   0.068     7.743   53.571   29.014
LGA    D   267_A      D   267_B     2.799     0    0.029   0.698     3.331   57.262   55.417
LGA    A   268_A      A   268_B     2.670     0    0.032   0.038     3.303   62.857   60.286
LGA    I   269_A      I   269_B     2.243     0    0.210   0.219     4.841   59.524   50.000
LGA    L   270_A      L   270_B     3.369     0    0.265   1.142     4.238   48.571   55.833
LGA    K   271_A      K   271_B     3.846     0    0.106   0.810     6.812   48.333   33.122
LGA    H   272_A      H   272_B     2.727     0    0.640   1.413     3.729   55.357   63.857
LGA    P   273_A      P   273_B     6.216     0    0.131   0.457     9.340   29.524   18.912

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       50     200    200  100.00     396    396  100.00               594
SUMMARY(RMSD_GDC):     6.903          6.588                  7.914            3.133    2.700

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50  594    4.0     29    2.84     4.082     3.654     0.986

LGA_LOCAL      RMSD:   2.841  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.689  Number of assigned atoms:   50 
Std_ASGN_ATOMS RMSD:   6.903  Standard rmsd on all 50 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.921382 * X  +  -0.020879 * Y  +  -0.388098 * Z  +  -9.545924
  Y_new =   0.388537 * X  +  -0.024454 * Y  +  -0.921109 * Z  +  -5.004373
  Z_new =   0.009742 * X  +  -0.999483 * Y  +   0.030644 * Z  +  48.377377 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.742530 -0.009742 -1.540146   [DEG:  157.1354   -0.5582  -88.2439 ]
ZXZ: -0.398764  1.540148  3.131846   [DEG:  -22.8475   88.2440  179.4416 ]
 
# END of job
