
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , 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      30_A - 58_A        4.62    15.09
  LCS_AVERAGE:     43.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.48    15.34
  LCS_AVERAGE:     33.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.72    15.34
  LCS_AVERAGE:     29.37

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     1_A     A     1_A      3   14   17      3    3    3    5    8   22   32   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     18   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     18   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17      3   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   25      3   16   32   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3   12   23   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   17   25     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   17   25      3    3    4    6   12   21   25   33   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   17   25      3   14   14   14   15   15   21   25   32   38   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   17   25      5   14   14   14   15   15   16   19   20   22   22   22   24   34   35   41   44   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   33   37   38 
LCS_GDT     P    19_A     P    19_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     F    20_A     F    20_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     K    21_A     K    21_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     K    22_A     K    22_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     G    23_A     G    23_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     E    24_A     E    24_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     I    25_A     I    25_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     L    26_A     L    26_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     R    27_A     R    27_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   29   30 
LCS_GDT     I    28_A     I    28_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   27   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   16   19   20   22   22   22   22   24   26   29   32   34   37   40 
LCS_GDT     D    30_A     D    30_A     15   17   29      3    4    9   14   15   15   16   19   20   22   22   25   27   30   33   35   43   45   46   46 
LCS_GDT     K    31_A     K    31_A      3   16   29      3    3    4    4    8   11   16   19   20   22   23   25   27   36   42   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      3    7   29      3    3    4    6    7   15   16   19   20   22   22   25   29   37   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      3    7   29      3    3    4    5    7    9   13   24   31   38   39   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      3   25   29      3    3    5    5   14   17   26   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   34   34   36   36   37   37   37   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     30   34   34   36   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    4    8   23   36   37   37   38   39   40   41   42   42   42   43   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.59  (  29.37   33.47   43.94 )

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     30     34     34     36     36     37     37     38     39     40     41     42     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  51.72  58.62  58.62  62.07  62.07  63.79  63.79  65.52  67.24  68.97  70.69  72.41  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.32   0.42   0.42   0.75   0.75   0.90   0.90   1.68   1.67   2.04   2.36   2.75   2.75   2.75   3.23   3.68   3.68   4.02   4.45   4.45
GDT RMS_ALL_AT  15.35  15.36  15.36  15.41  15.41  15.39  15.39  15.30  15.30  15.20  15.09  15.06  15.06  15.06  15.01  14.92  14.92  14.79  14.68  14.68

# Checking swapping
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    33_A      E    33_A
#   possible swapping detected:  E    34_A      E    34_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     5.859     0    0.257   0.270     7.741   30.476   27.810
LGA    E     2_A      E     2_A     1.011     0    0.660   1.032     7.694   83.810   48.360
LGA    Y     3_A      Y     3_A     0.572     0    0.024   0.124     0.863   90.476   92.063
LGA    V     4_A      V     4_A     0.511     0    0.029   0.045     0.701   92.857   91.837
LGA    R     5_A      R     5_A     0.317     0    0.026   0.071     0.375  100.000  100.000
LGA    A     6_A      A     6_A     0.181     0    0.064   0.068     0.325  100.000  100.000
LGA    L     7_A      L     7_A     0.431     0    0.023   0.065     0.609   97.619   96.429
LGA    F     8_A      F     8_A     0.457     0    0.055   0.075     1.195   97.619   91.472
LGA    D     9_A      D     9_A     0.513     0    0.012   0.236     1.823   97.619   91.905
LGA    H    10_A      H    10_A     0.381     0    0.096   0.280     0.745   95.238   95.238
LGA    T    11_A      T    11_A     0.987     0    0.628   0.956     3.323   82.143   76.122
LGA    G    12_A      G    12_A     1.989     0    0.022   0.022     1.989   72.857   72.857
LGA    H    13_A      H    13_A     2.269     0    0.537   1.279     4.808   57.857   52.238
LGA    D    14_A      D    14_A     1.583     0    0.025   1.089     5.151   58.214   54.226
LGA    E    15_A      E    15_A     7.933     0    0.675   1.249    14.292   10.714    4.815
LGA    Q    16_A      Q    16_A     8.700     0    0.669   1.414    13.494    2.024    1.376
LGA    E    17_A      E    17_A    12.380     0    0.126   0.869    15.934    0.000    0.000
LGA    L    18_A      L    18_A    19.710     0    0.022   1.139    23.692    0.000    0.000
LGA    P    19_A      P    19_A    25.511     0    0.011   0.067    28.223    0.000    0.000
LGA    F    20_A      F    20_A    31.232     0    0.021   1.444    33.394    0.000    0.000
LGA    K    21_A      K    21_A    38.091     0    0.011   0.848    43.017    0.000    0.000
LGA    K    22_A      K    22_A    41.033     0    0.092   0.481    50.067    0.000    0.000
LGA    G    23_A      G    23_A    42.781     0    0.033   0.033    42.781    0.000    0.000
LGA    E    24_A      E    24_A    39.017     0    0.056   1.035    39.973    0.000    0.000
LGA    I    25_A      I    25_A    36.656     0    0.079   0.101    43.037    0.000    0.000
LGA    L    26_A      L    26_A    30.173     0    0.009   0.084    32.225    0.000    0.000
LGA    R    27_A      R    27_A    28.297     0    0.020   1.196    33.385    0.000    0.000
LGA    I    28_A      I    28_A    21.120     0    0.045   0.622    23.858    0.000    0.000
LGA    R    29_A      R    29_A    20.507     0    0.589   1.208    29.483    0.000    0.000
LGA    D    30_A      D    30_A    16.500     0    0.704   1.273    19.996    0.000    0.000
LGA    K    31_A      K    31_A    14.273     0    0.294   0.303    21.420    0.000    0.000
LGA    P    32_A      P    32_A    13.226     0    0.091   0.327    15.912    0.000    0.000
LGA    E    33_A      E    33_A    10.179     0    0.724   0.884    12.429    1.905    0.847
LGA    E    34_A      E    34_A     5.648     0    0.219   0.888     8.133   28.333   17.354
LGA    Q    35_A      Q    35_A     1.353     0    0.660   1.185     3.645   81.429   64.921
LGA    L    36_A      L    36_A     1.493     0    0.167   0.563     2.393   75.119   72.976
LGA    W    37_A      W    37_A     1.214     0    0.016   0.233     2.366   85.952   78.503
LGA    N    38_A      N    38_A     0.949     0    0.044   0.841     2.892   88.214   80.714
LGA    A    39_A      A    39_A     0.484     0    0.037   0.049     0.596   97.619   98.095
LGA    E    40_A      E    40_A     0.466     0    0.020   0.523     2.393   97.619   89.788
LGA    N    41_A      N    41_A     0.480     0    0.012   0.124     1.060   92.976   94.107
LGA    V    42_A      V    42_A     0.966     0    0.044   1.149     3.476   85.952   78.299
LGA    E    43_A      E    43_A     1.087     0    0.059   0.120     1.430   81.429   85.450
LGA    G    44_A      G    44_A     1.217     0    0.031   0.031     1.217   81.429   81.429
LGA    K    45_A      K    45_A     0.855     0    0.022   0.356     1.060   90.595   88.519
LGA    R    46_A      R    46_A     0.279     0    0.037   0.238     3.091  100.000   83.160
LGA    G    47_A      G    47_A     0.302     0    0.020   0.020     0.539   97.619   97.619
LGA    L    48_A      L    48_A     0.765     0    0.049   0.056     0.907   90.476   90.476
LGA    I    49_A      I    49_A     0.822     0    0.000   0.095     1.042   88.214   89.345
LGA    H    50_A      H    50_A     1.254     0    0.038   0.121     1.960   81.429   78.000
LGA    V    51_A      V    51_A     1.121     0    0.051   0.076     1.320   85.952   84.014
LGA    V    52_A      V    52_A     1.020     0    0.033   0.074     1.610   88.214   82.857
LGA    L    53_A      L    53_A     0.683     0    0.024   0.098     1.421   95.238   90.595
LGA    V    54_A      V    54_A     0.235     0    0.063   0.079     0.485  100.000  100.000
LGA    E    55_A      E    55_A     0.619     0    0.031   0.074     0.636   90.476   93.651
LGA    K    56_A      K    56_A     0.623     0    0.031   1.248     5.812   95.238   74.868
LGA    Y    57_A      Y    57_A     0.412     0    0.583   0.487     1.957   93.214   90.794
LGA    G    58_A      G    58_A     3.124     0    0.648   0.648     4.104   46.905   46.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.127         13.055                 13.512           57.087   53.966

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.68    65.517    57.521     2.132

LGA_LOCAL      RMSD:   1.682  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.301  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.127  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.409947 * X  +  -0.618356 * Y  +  -0.670506 * Z  +  90.140587
  Y_new =   0.910601 * X  +  -0.319722 * Y  +  -0.261886 * Z  + 154.812256
  Z_new =  -0.052436 * X  +  -0.717923 * Y  +   0.694145 * Z  +  57.460163 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.993812  0.052461 -0.802236   [DEG:  114.2370    3.0058  -45.9647 ]
ZXZ: -1.198437  0.803565 -3.068683   [DEG:  -68.6654   46.0409 -175.8226 ]
 
# END of job
