
#######################################################
#                                                     #
#                        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:    49       1_F - 49_F        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       2_F - 26_F        0.96     2.01
  LONGEST_CONTINUOUS_SEGMENT:    25       3_F - 27_F        0.87     2.01
  LCS_AVERAGE:     33.82

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      6   49   49      4    4    8   18   37   46   47   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     25   49   49      4    5   24   37   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     25   49   49      4   23   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     25   49   49      5   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     25   49   49     14   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     25   49   49      3   24   34   37   42   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     25   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     25   49   49      3   26   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     25   49   49     14   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     25   49   49      5    5   32   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     25   49   49     15   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     25   49   49      5    9   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F      6   49   49      5    5    8   28   42   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F      6   49   49      5    5    8   14   35   44   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F      4   49   49      4    7   17   35   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F      6   49   49      7   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F      6   49   49      6   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F      6   49   49      8   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F      6   49   49      3   15   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F      6   49   49      3    4    9   33   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F      6   49   49      3    4   20   36   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F      5   49   49      3    9   23   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F      9   49   49      5   16   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F      9   49   49      8   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F      9   49   49      4   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F      9   49   49     14   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F      9   49   49     16   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F      9   49   49      8   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F      9   49   49      4   27   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F      9   49   49      9   25   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F      9   49   49      3   28   34   39   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F      9   49   49      3    6   17   34   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F      6   49   49      3    4   17   31   44   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3   49   49      3    8   23   39   42   46   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  77.94  (  33.82  100.00  100.00 )

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     16     28     34     39     44     46     48     49     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  32.65  57.14  69.39  79.59  89.80  93.88  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.25   0.62   0.81   1.15   1.50   1.54   1.69   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_AT   2.15   1.95   1.92   1.87   1.79   1.80   1.79   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  F     8_F      F     8_F
#   possible swapping detected:  D    11_F      D    11_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     4.016     0    0.071   1.230     5.330   35.952   38.333
LGA    G     2_F      G     2_F     2.429     0    0.070   0.070     2.600   69.048   69.048
LGA    K     3_F      K     3_F     1.121     0    0.050   1.019     7.860   85.952   59.259
LGA    I     4_F      I     4_F     1.655     0    0.149   1.030     6.254   71.071   54.167
LGA    K     5_F      K     5_F     0.494     0    0.152   1.046     2.351   86.429   81.852
LGA    R     6_F      R     6_F     1.040     0    0.039   0.941     4.741   83.690   65.844
LGA    F     7_F      F     7_F     1.346     0    0.076   0.214     2.779   81.429   70.909
LGA    F     8_F      F     8_F     1.315     0    0.094   0.801     4.854   81.429   63.074
LGA    A     9_F      A     9_F     1.442     0    0.104   0.135     2.032   75.119   76.381
LGA    K    10_F      K    10_F     2.118     0    0.041   1.083     4.638   68.810   62.963
LGA    D    11_F      D    11_F     0.706     0    0.080   0.866     3.896   88.214   73.393
LGA    M    12_F      M    12_F     0.660     0    0.031   1.204     3.374   90.476   78.155
LGA    R    13_F      R    13_F     0.708     0    0.041   1.895     8.374   90.476   59.351
LGA    A    14_F      A    14_F     0.852     0    0.022   0.021     0.904   90.476   90.476
LGA    A    15_F      A    15_F     0.871     0    0.036   0.034     0.922   90.476   90.476
LGA    L    16_F      L    16_F     0.534     0    0.022   1.119     3.051   95.238   85.655
LGA    A    17_F      A    17_F     0.497     0    0.054   0.059     0.626   97.619   96.190
LGA    Q    18_F      Q    18_F     0.866     0    0.018   0.330     2.083   90.476   84.603
LGA    V    19_F      V    19_F     0.823     0    0.022   0.075     0.823   90.476   90.476
LGA    K    20_F      K    20_F     0.636     0    0.032   0.978     4.075   90.476   77.143
LGA    D    21_F      D    21_F     0.680     0    0.027   0.888     3.082   90.476   78.036
LGA    T    22_F      T    22_F     0.784     0    0.098   1.128     2.341   88.214   81.837
LGA    L    23_F      L    23_F     1.532     0    0.222   1.070     5.428   83.810   70.536
LGA    G    24_F      G    24_F     0.547     0    0.022   0.022     1.186   88.214   88.214
LGA    S    25_F      S    25_F     2.044     0    0.086   0.089     2.779   70.952   66.349
LGA    D    26_F      D    26_F     0.905     0    0.038   0.110     1.308   83.690   84.821
LGA    A    27_F      A    27_F     1.744     0    0.047   0.045     2.561   69.048   69.810
LGA    V    28_F      V    28_F     3.050     0    0.624   0.993     4.748   50.476   46.667
LGA    I    29_F      I    29_F     4.054     0    0.067   0.487    10.856   45.595   26.310
LGA    M    30_F      M    30_F     2.400     0    0.630   0.961    10.788   73.214   42.738
LGA    S    31_F      S    31_F     0.855     0    0.091   0.510     1.961   83.810   81.587
LGA    N    32_F      N    32_F     1.298     0    0.435   1.100     4.358   75.476   63.452
LGA    K    33_F      K    33_F     1.351     0    0.155   1.246     4.551   83.690   63.968
LGA    K    34_F      K    34_F     1.714     0    0.105   0.684     6.427   73.214   57.302
LGA    V    35_F      V    35_F     3.109     0    0.047   1.197     5.316   57.262   50.816
LGA    N    36_F      N    36_F     3.033     0    0.652   0.511     5.582   48.571   40.952
LGA    G    37_F      G    37_F     2.649     0    0.143   0.143     2.649   62.857   62.857
LGA    G    38_F      G    38_F     1.528     0    0.055   0.055     1.661   77.143   77.143
LGA    I    39_F      I    39_F     0.801     0    0.098   1.458     4.525   85.952   72.560
LGA    E    40_F      E    40_F     1.189     0    0.137   0.386     3.704   83.690   69.365
LGA    I    41_F      I    41_F     1.179     0    0.049   1.241     3.122   81.429   75.357
LGA    V    42_F      V    42_F     1.034     0    0.027   1.153     3.615   81.429   74.762
LGA    A    43_F      A    43_F     1.287     0    0.135   0.177     1.745   81.429   79.714
LGA    A    44_F      A    44_F     1.309     0    0.066   0.084     1.597   79.286   79.714
LGA    V    45_F      V    45_F     1.118     0    0.136   0.375     1.987   85.952   84.082
LGA    L    46_F      L    46_F     0.814     0    0.639   0.570     4.422   70.714   72.143
LGA    E    47_F      E    47_F     2.610     0    0.586   0.541     7.785   63.214   40.423
LGA    H    48_F      H    48_F     3.003     0    0.174   1.206    10.430   55.476   27.095
LGA    H    49_F      H    49_F     2.765     0    0.548   1.296     6.110   46.786   46.048

# 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):     1.777          1.852                  2.985           77.029   68.212

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     49    1.78    84.184    91.738     2.611

LGA_LOCAL      RMSD:   1.777  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.777  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.777  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.360274 * X  +  -0.379244 * Y  +   0.852277 * Z  +  61.699547
  Y_new =  -0.909472 * X  +   0.346041 * Y  +  -0.230471 * Z  + -66.849709
  Z_new =  -0.207518 * X  +  -0.858155 * Y  +  -0.469582 * Z  +   7.166292 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.947967  0.209037 -2.071487   [DEG: -111.6103   11.9770 -118.6874 ]
ZXZ:  1.306696  2.059613 -2.904328   [DEG:   74.8681  118.0071 -166.4057 ]
 
# END of job
