
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       7_F - 49_F        4.74    10.19
  LCS_AVERAGE:     79.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      11_F - 27_F        1.91    12.47
  LCS_AVERAGE:     23.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.91    13.47
  LCS_AVERAGE:     17.03

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      4    5    7      3    3    4    4    4    5    6    6    6    6    9    9    9   11   12   17   19   20   22   23 
LCS_GDT     G     2_F     G     2_F      4    5    8      3    3    4    4    4    5    6    6    6    6    9    9    9   15   16   17   21   21   22   23 
LCS_GDT     K     3_F     K     3_F      4    5   13      3    3    4    4    4    5    6    6    7    8   11   13   15   16   16   17   21   21   22   23 
LCS_GDT     I     4_F     I     4_F      4    5   13      0    3    4    4    4    5    6    6    7    8   11   13   15   16   16   17   21   21   22   23 
LCS_GDT     K     5_F     K     5_F      3    5   13      0    3    3    4    4    5    6    6    7    9   11   13   15   16   16   18   21   22   22   24 
LCS_GDT     R     6_F     R     6_F      3    4   13      1    3    5    5    5    5    6    7    8   11   11   13   15   16   18   20   23   23   25   28 
LCS_GDT     F     7_F     F     7_F      3    3   43      0    3    5    5    5    5    6    7    9   11   11   15   19   22   25   27   31   35   38   43 
LCS_GDT     F     8_F     F     8_F      3    4   43      0    3    5    5    5    9   11   13   17   23   33   34   40   41   42   42   42   42   42   43 
LCS_GDT     A     9_F     A     9_F      4    4   43      3    3    4    5    5    8   11   15   21   32   36   39   41   41   42   42   42   42   42   43 
LCS_GDT     K    10_F     K    10_F      4   16   43      3    3    4    5    8   14   16   22   28   34   37   39   41   41   42   42   42   42   42   43 
LCS_GDT     D    11_F     D    11_F     15   17   43      3   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     M    12_F     M    12_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     R    13_F     R    13_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    14_F     A    14_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    15_F     A    15_F     15   17   43      9   13   13   15   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     L    16_F     L    16_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    17_F     A    17_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     Q    18_F     Q    18_F     15   17   43      9   13   13   15   17   22   22   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     V    19_F     V    19_F     15   17   43      9   13   13   15   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     K    20_F     K    20_F     15   17   43      9   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     D    21_F     D    21_F     15   17   43      4   13   13   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     T    22_F     T    22_F     15   17   43      3   13   13   15   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     L    23_F     L    23_F     15   17   43      3   13   13   15   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     G    24_F     G    24_F     15   17   43      0    3   10   15   16   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     S    25_F     S    25_F     15   17   43      3    3   13   15   15   15   17   22   30   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     D    26_F     D    26_F      4   17   43      3    3    6   10   14   15   20   26   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    27_F     A    27_F      6   17   43      4    5    5    8   10   15   18   23   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     V    28_F     V    28_F      6    8   43      4    5    5    8   10   15   18   23   28   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     I    29_F     I    29_F      6    8   43      4    5    5    7   10   15   18   23   29   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     M    30_F     M    30_F      6    8   43      4    5    5    7    9   15   18   26   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     S    31_F     S    31_F      6    8   43      3    5    5    7    9   10   18   26   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     N    32_F     N    32_F      6    8   43      3    4    5    6    7    7    8   10   15   26   37   39   41   41   42   42   42   42   42   43 
LCS_GDT     K    33_F     K    33_F      4    7   43      3    4    4    5    9   15   22   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     K    34_F     K    34_F      4    6   43      3    4    5    6    9    9   11   21   29   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     V    35_F     V    35_F      4    6   43      3    4    5    5    9    9   16   25   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     N    36_F     N    36_F      4    9   43      3    4    4    8   10   12   17   26   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     G    37_F     G    37_F      4   12   43      3    4    7   13   14   21   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     G    38_F     G    38_F      8   12   43      5    6    8   12   16   17   19   23   30   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     I    39_F     I    39_F      8   12   43      5    6    8   12   16   21   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     E    40_F     E    40_F      8   12   43      5    6    8   13   16   21   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     I    41_F     I    41_F      8   12   43      5    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     V    42_F     V    42_F      8   12   43      5    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    43_F     A    43_F      8   12   43      4    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     A    44_F     A    44_F      8   12   43      5    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     V    45_F     V    45_F      8   12   43      5    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     L    46_F     L    46_F      7   12   43      4    8   11   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     E    47_F     E    47_F      7   12   43      0    4    8   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     H    48_F     H    48_F      7   12   43      0    3   10   16   18   22   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_GDT     H    49_F     H    49_F      3   11   43      1    2    4   10   14   20   25   27   31   35   38   39   41   41   42   42   42   42   42   43 
LCS_AVERAGE  LCS_A:  40.16  (  17.03   23.66   79.80 )

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      9     13     13     16     18     22     25     27     31     35     38     39     41     41     42     42     42     42     42     43 
GDT PERCENT_AT  18.37  26.53  26.53  32.65  36.73  44.90  51.02  55.10  63.27  71.43  77.55  79.59  83.67  83.67  85.71  85.71  85.71  85.71  85.71  87.76
GDT RMS_LOCAL    0.28   0.59   0.59   1.37   1.54   1.87   2.37   2.59   3.09   3.53   3.69   3.79   4.01   4.01   4.21   4.21   4.21   4.21   4.21   4.74
GDT RMS_ALL_AT  13.41  12.98  12.98  11.63  11.61  11.57  11.30  11.15  10.82  10.52  10.58  10.52  10.43  10.43  10.33  10.33  10.33  10.33  10.33  10.19

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    47_F      E    47_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F    33.368     0    0.266   0.786    37.534    0.000    0.000
LGA    G     2_F      G     2_F    31.705     0    0.058   0.058    32.427    0.000    0.000
LGA    K     3_F      K     3_F    31.730     0    0.639   1.077    33.972    0.000    0.000
LGA    I     4_F      I     4_F    27.931     0    0.240   1.074    31.450    0.000    0.000
LGA    K     5_F      K     5_F    23.189     0    0.622   1.032    28.651    0.000    0.000
LGA    R     6_F      R     6_F    21.306     0    0.584   0.795    25.078    0.000    0.000
LGA    F     7_F      F     7_F    17.079     0    0.604   1.507    19.686    0.000    0.000
LGA    F     8_F      F     8_F    11.130     0    0.570   1.481    13.599    0.476    0.736
LGA    A     9_F      A     9_F     8.641     0    0.597   0.587     9.698    7.857    6.381
LGA    K    10_F      K    10_F     6.965     0    0.057   1.536    11.060   20.238   11.217
LGA    D    11_F      D    11_F     1.803     0    0.576   1.448     4.040   62.976   54.940
LGA    M    12_F      M    12_F     2.997     0    0.023   1.149     9.635   60.952   40.774
LGA    R    13_F      R    13_F     1.374     0    0.070   1.636    10.491   86.190   50.563
LGA    A    14_F      A    14_F     1.837     0    0.022   0.032     2.788   73.214   70.000
LGA    A    15_F      A    15_F     3.069     0    0.053   0.059     3.700   55.476   53.048
LGA    L    16_F      L    16_F     1.799     0    0.041   1.237     6.329   81.667   65.595
LGA    A    17_F      A    17_F     1.606     0    0.041   0.045     2.683   75.595   71.905
LGA    Q    18_F      Q    18_F     3.758     0    0.047   0.954     7.237   48.452   32.857
LGA    V    19_F      V    19_F     2.997     0    0.036   0.120     4.630   62.976   51.973
LGA    K    20_F      K    20_F     0.625     0    0.036   1.005     7.206   90.476   65.608
LGA    D    21_F      D    21_F     2.388     0    0.036   0.864     6.061   64.881   47.440
LGA    T    22_F      T    22_F     2.842     0    0.060   1.064     5.039   59.048   52.789
LGA    L    23_F      L    23_F     2.492     0    0.611   0.779     6.001   68.929   51.429
LGA    G    24_F      G    24_F     2.567     0    0.360   0.360     5.542   45.119   45.119
LGA    S    25_F      S    25_F     6.269     0    0.645   0.796    10.096   27.976   19.127
LGA    D    26_F      D    26_F     5.574     0    0.150   0.909     8.157   20.357   14.940
LGA    A    27_F      A    27_F     5.960     0    0.078   0.139     6.202   19.286   19.714
LGA    V    28_F      V    28_F     6.848     0    0.194   1.011     9.418   13.333   11.156
LGA    I    29_F      I    29_F     6.671     0    0.042   0.689     8.771   13.333   12.024
LGA    M    30_F      M    30_F     5.910     0    0.073   0.774     6.967   20.357   18.274
LGA    S    31_F      S    31_F     5.875     0    0.172   0.676     7.806   16.310   15.635
LGA    N    32_F      N    32_F     7.635     0    0.051   1.145    10.557   15.833    8.631
LGA    K    33_F      K    33_F     4.793     0    0.629   1.012    14.198   22.262   13.439
LGA    K    34_F      K    34_F     7.051     0    0.616   0.873    12.169   15.476    8.360
LGA    V    35_F      V    35_F     6.627     0    0.126   0.881     8.581   22.500   15.714
LGA    N    36_F      N    36_F     5.657     0    0.618   1.082    11.874   26.786   14.702
LGA    G    37_F      G    37_F     3.169     0    0.421   0.421     3.970   48.452   48.452
LGA    G    38_F      G    38_F     5.121     0    0.156   0.156     5.121   35.952   35.952
LGA    I    39_F      I    39_F     3.489     0    0.040   1.144     4.594   40.476   41.964
LGA    E    40_F      E    40_F     3.402     0    0.147   1.078     4.190   61.548   52.328
LGA    I    41_F      I    41_F     1.544     0    0.055   1.090     4.860   69.048   61.845
LGA    V    42_F      V    42_F     0.186     0    0.143   0.210     1.885   90.833   84.354
LGA    A    43_F      A    43_F     0.839     0    0.068   0.103     1.754   90.476   86.952
LGA    A    44_F      A    44_F     0.318     0    0.115   0.138     1.140   95.357   96.286
LGA    V    45_F      V    45_F     0.681     0    0.099   0.261     2.790   86.071   75.918
LGA    L    46_F      L    46_F     1.365     0    0.605   1.042     4.799   70.000   66.310
LGA    E    47_F      E    47_F     3.055     0    0.568   1.037     6.500   49.048   39.683
LGA    H    48_F      H    48_F     3.122     0    0.610   1.073     8.608   52.262   28.333
LGA    H    49_F      H    49_F     4.047     0    0.043   0.267     5.715   38.214   49.667

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):     9.554          9.380                 10.292           41.348   34.942

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     27    2.59    50.000    45.710     1.005

LGA_LOCAL      RMSD:   2.586  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.152  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   9.554  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.725807 * X  +  -0.585479 * Y  +   0.361134 * Z  +  33.418335
  Y_new =   0.520608 * X  +   0.810662 * Y  +   0.267947 * Z  + -119.250107
  Z_new =  -0.449635 * X  +  -0.006468 * Y  +   0.893189 * Z  + -15.747526 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.622230  0.466357 -0.007242   [DEG:   35.6512   26.7203   -0.4149 ]
ZXZ:  2.209131  0.466409 -1.585181   [DEG:  126.5739   26.7232  -90.8242 ]
 
# END of job
