
#######################################################
#                                                     #
#                        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   56 (  400),  selected   56 , name one
# Molecule2: number of CA atoms  194 ( 1449),  selected   56 , 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:    29      25_A - 53_A        4.57    17.99
  LONGEST_CONTINUOUS_SEGMENT:    29      26_A - 54_A        4.94    18.29
  LCS_AVERAGE:     13.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      51_A - 68_A        1.84    14.51
  LCS_AVERAGE:      6.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      28_A - 41_A        0.38    16.74
  LCS_AVERAGE:      4.80

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   56
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     S    25_A     S    25_A      4    4   29      3    4    4    5    5    5    6    8   10   11   12   14   23   27   28   28   29   29   29   30 
LCS_GDT     D    26_A     D    26_A      4    4   29      3    4    4    5    8   12   13   17   20   23   24   27   28   28   28   29   29   29   29   31 
LCS_GDT     Y    27_A     Y    27_A      4   15   29      3    4    4    5    7    9   13   17   20   23   24   27   28   28   28   29   29   32   35   36 
LCS_GDT     S    28_A     S    28_A     14   15   29      9   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   29   32   35   36 
LCS_GDT     E    29_A     E    29_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   29   31   35   36 
LCS_GDT     I    30_A     I    30_A     14   15   29     12   14   14   14   14   14   15   15   18   24   24   27   28   28   28   29   30   32   35   36 
LCS_GDT     T    31_A     T    31_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   30   33   35   39 
LCS_GDT     I    32_A     I    32_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   29   31   35   36 
LCS_GDT     H    33_A     H    33_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   29   32   35   36 
LCS_GDT     L    34_A     L    34_A     14   15   29     12   14   14   14   14   14   15   16   20   24   24   27   28   28   30   32   35   36   37   39 
LCS_GDT     L    35_A     L    35_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   28   29   30   32   35   39 
LCS_GDT     H    36_A     H    36_A     14   15   29     12   14   14   14   14   14   15   16   20   24   24   27   28   28   28   29   29   31   34   35 
LCS_GDT     Q    37_A     Q    37_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   28   31   34   35   36   37   39 
LCS_GDT     L    38_A     L    38_A     14   15   29     12   14   14   14   14   14   15   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     V    39_A     V    39_A     14   15   29     12   14   14   14   14   14   15   15   16   19   23   27   28   28   28   29   31   33   37   39 
LCS_GDT     L    40_A     L    40_A     14   15   29     12   14   14   14   14   14   15   16   20   24   24   27   28   28   31   34   35   36   37   39 
LCS_GDT     A    41_A     A    41_A     14   15   29     11   14   14   14   14   14   15   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     C    42_A     C    42_A      4   15   29      3    4    5    6   10   12   15   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     G    43_A     G    43_A      4    9   29      3    4    5    6   10   12   14   17   20   24   24   27   28   28   28   30   32   35   37   39 
LCS_GDT     D    44_A     D    44_A      4    9   29      3    4    5    8    8   11   14   17   20   24   24   27   28   28   28   29   29   30   33   35 
LCS_GDT     V    45_A     V    45_A      7    9   29      3    4    7    8   10   12   14   17   20   24   24   27   28   28   28   31   34   36   37   39 
LCS_GDT     S    46_A     S    46_A      7    9   29      3    6    7    8    9   12   14   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     L    47_A     L    47_A      7    9   29      5    6    7    8   10   12   14   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     V    48_A     V    48_A      7    9   29      5    6    7    8   10   12   14   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     N    49_A     N    49_A      7    9   29      5    6    7    8   10   12   14   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     A    50_A     A    50_A      7    9   29      5    6    7    8   10   12   14   17   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     V    51_A     V    51_A      7   18   29      5    6    7    9   11   14   18   18   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     R    52_A     R    52_A      6   18   29      3    5    9   14   16   17   18   18   20   24   24   27   28   30   31   34   35   36   37   39 
LCS_GDT     L    53_A     L    53_A      6   18   29      3    5   12   14   16   17   18   18   19   21   22   25   28   30   31   34   35   36   37   39 
LCS_GDT     S    54_A     S    54_A      6   18   29      4    8   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     Q    55_A     Q    55_A      6   18   26      3    4    7   11   16   17   18   18   19   21   22   23   26   29   31   34   35   36   37   39 
LCS_GDT     G    56_A     G    56_A     13   18   26      3    4    7   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    57_A     A    57_A     13   18   26      8   12   12   14   15   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     I    58_A     I    58_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    59_A     A    59_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     S    60_A     S    60_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    61_A     A    61_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     R    62_A     R    62_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     D    63_A     D    63_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    64_A     A    64_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     L    65_A     L    65_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     K    66_A     K    66_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   22   26   29   31   34   35   36   37   39 
LCS_GDT     A    67_A     A    67_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     G    68_A     G    68_A     13   18   26     11   12   12   14   16   17   18   18   19   21   22   23   26   30   31   34   35   36   37   39 
LCS_GDT     C    69_A     C    69_A      4   14   26      3    4    4    6    6    9   14   16   19   20   21   23   26   30   31   34   35   36   37   39 
LCS_GDT     P    70_A     P    70_A      4    6   26      3    4    4    6    7   11   11   13   16   19   21   23   26   30   31   34   35   36   37   39 
LCS_GDT     V    71_A     V    71_A      4    6   26      3    4    4    6    7   11   11   13   15   19   21   23   26   30   31   34   35   36   37   39 
LCS_GDT     V    72_A     V    72_A      4    6   23      3    4    4    6    6    7    8   10   12   16   18   18   21   22   24   28   30   33   37   39 
LCS_GDT     T    73_A     T    73_A      4    6   23      3    4    4    6    6    6    8   10   12   16   18   19   21   22   24   28   30   33   36   39 
LCS_GDT     D    74_A     D    74_A      4    7   23      3    4    4    4    5    7    8    8   10   11   13   18   21   21   23   24   28   32   35   39 
LCS_GDT     V    75_A     V    75_A      6    7   23      6    6    6    6    6    7    8    8   11   14   16   19   21   22   25   28   30   33   37   39 
LCS_GDT     P    76_A     P    76_A      6    7   23      6    6    6    6    6    7    7    8    8   11   12   19   21   24   27   30   32   35   37   39 
LCS_GDT     V    77_A     V    77_A      6    7   14      6    6    6    6    6    7    7    8    8    9   14   17   19   20   23   30   32   35   37   39 
LCS_GDT     V    78_A     V    78_A      6    7   14      6    6    6    7    8   11   11   13   15   19   21   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    79_A     A    79_A      6    7   14      6    6    6    7    8   11   11   13   16   19   21   23   26   30   31   34   35   36   37   39 
LCS_GDT     A    80_A     A    80_A      6    7   14      6    6    6    6    8    9   10   12   15   18   21   23   26   30   31   34   35   36   37   39 
LCS_AVERAGE  LCS_A:   8.39  (   4.80    6.73   13.65 )

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     14     14     16     17     18     18     20     24     24     27     28     30     31     34     35     36     37     39 
GDT PERCENT_AT   6.19   7.22   7.22   7.22   8.25   8.76   9.28   9.28  10.31  12.37  12.37  13.92  14.43  15.46  15.98  17.53  18.04  18.56  19.07  20.10
GDT RMS_LOCAL    0.27   0.38   0.38   0.38   1.40   1.50   1.84   1.84   3.04   3.77   3.72   4.07   4.35   5.07   5.11   5.53   5.66   5.82   6.01   6.37
GDT RMS_ALL_AT  16.77  16.74  16.74  16.74  14.73  14.75  14.51  14.51  16.24  17.97  17.54  17.73  17.95  11.59  11.76  11.70  11.65  11.59  11.57  11.45

# Checking swapping
#   possible swapping detected:  D    26_A      D    26_A
#   possible swapping detected:  Y    27_A      Y    27_A
#   possible swapping detected:  D    74_A      D    74_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S    25_A      S    25_A    26.468     0    0.054   0.618    28.058    0.000    0.000
LGA    D    26_A      D    26_A    24.886     0    0.119   0.994    28.003    0.000    0.000
LGA    Y    27_A      Y    27_A    19.412     0    0.657   1.090    21.432    0.000    0.000
LGA    S    28_A      S    28_A    21.954     0    0.537   0.921    23.250    0.000    0.000
LGA    E    29_A      E    29_A    20.338     0    0.047   0.855    28.606    0.000    0.000
LGA    I    30_A      I    30_A    14.080     0    0.000   0.121    16.616    0.000    0.000
LGA    T    31_A      T    31_A    13.087     0    0.007   1.096    15.839    0.000    0.000
LGA    I    32_A      I    32_A    15.326     0    0.052   0.729    21.203    0.000    0.000
LGA    H    33_A      H    33_A    10.581     0    0.039   1.532    14.502    3.690    1.476
LGA    L    34_A      L    34_A     6.984     0    0.048   0.149     9.157    6.905    8.690
LGA    L    35_A      L    35_A    11.947     0    0.050   1.408    16.937    0.000    0.000
LGA    H    36_A      H    36_A     9.853     0    0.010   0.872    14.710    2.024    0.857
LGA    Q    37_A      Q    37_A     6.713     0    0.037   0.962     9.754    7.500   10.899
LGA    L    38_A      L    38_A    12.258     0    0.050   1.215    15.203    0.119    0.060
LGA    V    39_A      V    39_A    14.900     0    0.091   1.230    17.997    0.000    0.000
LGA    L    40_A      L    40_A    10.659     0    0.071   0.141    12.194    0.000    4.226
LGA    A    41_A      A    41_A    15.335     0    0.264   0.293    18.934    0.000    0.000
LGA    C    42_A      C    42_A    17.296     0    0.641   0.930    20.886    0.000    0.000
LGA    G    43_A      G    43_A    20.895     0    0.699   0.699    20.895    0.000    0.000
LGA    D    44_A      D    44_A    21.155     0    0.540   1.496    25.032    0.000    0.000
LGA    V    45_A      V    45_A    16.344     0    0.106   1.159    19.062    0.000    0.000
LGA    S    46_A      S    46_A    14.204     0    0.036   0.151    17.222    0.000    0.000
LGA    L    47_A      L    47_A    11.596     0    0.121   0.775    13.530    1.310    0.655
LGA    V    48_A      V    48_A     9.443     0    0.046   0.103    12.534    5.476    3.129
LGA    N    49_A      N    49_A     7.117     0    0.172   0.366    11.042   15.833    9.048
LGA    A    50_A      A    50_A     7.658     0    0.099   0.106     9.528   12.857   10.381
LGA    V    51_A      V    51_A     4.440     0    0.635   0.490     5.527   32.024   29.524
LGA    R    52_A      R    52_A     1.773     0    0.355   1.281     4.531   77.381   60.260
LGA    L    53_A      L    53_A     1.325     0    0.204   0.778     5.718   83.690   61.310
LGA    S    54_A      S    54_A     0.965     0    0.103   0.463     3.456   90.595   80.873
LGA    Q    55_A      Q    55_A     2.467     0    0.646   0.980     5.499   59.405   46.561
LGA    G    56_A      G    56_A     2.367     0    0.154   0.154     3.108   65.238   65.238
LGA    A    57_A      A    57_A     2.732     0    0.322   0.333     3.745   64.881   60.571
LGA    I    58_A      I    58_A     1.730     0    0.057   0.220     2.227   77.381   75.179
LGA    A    59_A      A    59_A     0.668     0    0.020   0.040     0.964   92.857   92.381
LGA    S    60_A      S    60_A     0.927     0    0.052   0.094     1.298   90.476   87.460
LGA    A    61_A      A    61_A     1.274     0    0.070   0.083     2.055   81.429   78.095
LGA    R    62_A      R    62_A     1.091     0    0.058   1.136     2.172   83.690   77.619
LGA    D    63_A      D    63_A     0.461     0    0.018   0.125     0.871   97.619   94.048
LGA    A    64_A      A    64_A     0.393     0    0.028   0.038     1.113   92.976   94.381
LGA    L    65_A      L    65_A     1.176     0    0.039   0.130     1.597   81.548   80.417
LGA    K    66_A      K    66_A     1.366     0    0.019   1.052     5.666   79.286   64.444
LGA    A    67_A      A    67_A     1.448     0    0.117   0.131     2.219   75.119   76.381
LGA    G    68_A      G    68_A     1.778     0    0.350   0.350     4.746   57.262   57.262
LGA    C    69_A      C    69_A     7.479     0    0.686   0.616     8.972   11.786    9.524
LGA    P    70_A      P    70_A    11.524     0    0.457   0.628    14.468    0.119    0.136
LGA    V    71_A      V    71_A    15.206     0    0.031   0.214    17.582    0.000    0.000
LGA    V    72_A      V    72_A    22.116     0    0.627   0.947    25.011    0.000    0.000
LGA    T    73_A      T    73_A    24.530     0    0.022   1.216    27.575    0.000    0.000
LGA    D    74_A      D    74_A    26.629     0    0.041   0.956    27.996    0.000    0.000
LGA    V    75_A      V    75_A    29.761     0    0.521   1.437    33.684    0.000    0.000
LGA    P    76_A      P    76_A    26.462     0    0.026   0.144    30.708    0.000    0.000
LGA    V    77_A      V    77_A    22.713     0    0.028   0.967    24.588    0.000    0.000
LGA    V    78_A      V    78_A    19.994     0    0.088   0.097    22.014    0.000    0.000
LGA    A    79_A      A    79_A    19.854     0    0.114   0.130    21.808    0.000    0.000
LGA    A    80_A      A    80_A    16.538     0    0.630   0.606    18.074    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       56     224    224  100.00     400    400  100.00               194
SUMMARY(RMSD_GDC):    10.168          9.967                 11.066            7.477    6.913

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56  194    4.0     18    1.84    10.309     9.403     0.930

LGA_LOCAL      RMSD:   1.836  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.515  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:  10.168  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.107720 * X  +  -0.743433 * Y  +   0.660079 * Z  +  79.614716
  Y_new =  -0.356490 * X  +  -0.648674 * Y  +  -0.672411 * Z  + 108.452347
  Z_new =   0.928068 * X  +  -0.162879 * Y  +  -0.334902 * Z  + -26.812630 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.277351 -1.189192 -2.688925   [DEG:  -73.1868  -68.1357 -154.0641 ]
ZXZ:  0.776143  1.912297  1.744530   [DEG:   44.4697  109.5666   99.9542 ]
 
# END of job
