
#######################################################
#                                                     #
#                        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        1.46     1.46
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.46     1.46
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.87     1.51
  LCS_AVERAGE:     90.34

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      5   49   49      3    4    7   12   16   29   44   47   47   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      3   11   28   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      6   38   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     24   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49      6   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     27   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49      4   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49     27   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      7   26   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49      7   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49      7   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49      7   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49     24   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      4   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49      3   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      3   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     21   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     28   41   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      3   37   44   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      3   24   43   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     45   49   49      3    4    5    8   17   34   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3   49   49      0    3   25   45   46   47   48   48   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  96.78  (  90.34  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     28     41     44     45     46     47     48     48     48     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  57.14  83.67  89.80  91.84  93.88  95.92  97.96  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.50   0.62   0.72   0.83   0.97   1.17   1.17   1.17   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46
GDT RMS_ALL_AT   1.61   1.63   1.58   1.54   1.55   1.50   1.49   1.49   1.49   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    21_F      D    21_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    40_F      E    40_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     6.536     0    0.128   1.206     8.835   19.762   16.429
LGA    G     2_F      G     2_F     3.435     0    0.101   0.101     4.621   45.476   45.476
LGA    K     3_F      K     3_F     1.266     0    0.164   1.072     5.663   81.548   63.175
LGA    I     4_F      I     4_F     0.773     0    0.070   0.121     1.613   90.476   86.012
LGA    K     5_F      K     5_F     0.190     0    0.024   0.992     2.706  100.000   84.392
LGA    R     6_F      R     6_F     0.535     0    0.018   0.651     2.820   92.857   75.974
LGA    F     7_F      F     7_F     0.517     0    0.029   0.118     0.668   90.476   93.074
LGA    F     8_F      F     8_F     0.543     0    0.037   1.264     6.741   90.476   61.212
LGA    A     9_F      A     9_F     0.424     0    0.042   0.056     0.471  100.000  100.000
LGA    K    10_F      K    10_F     0.567     0    0.029   0.995     4.475   95.238   77.460
LGA    D    11_F      D    11_F     1.035     0    0.080   1.018     3.699   88.214   74.821
LGA    M    12_F      M    12_F     0.682     0    0.031   1.092     4.162   95.238   82.024
LGA    R    13_F      R    13_F     0.255     0    0.061   1.585     7.531  100.000   67.576
LGA    A    14_F      A    14_F     0.238     0    0.025   0.041     0.355  100.000  100.000
LGA    A    15_F      A    15_F     0.277     0    0.054   0.058     0.392  100.000  100.000
LGA    L    16_F      L    16_F     0.258     0    0.016   1.080     2.513  100.000   89.048
LGA    A    17_F      A    17_F     0.428     0    0.058   0.064     0.609  100.000   98.095
LGA    Q    18_F      Q    18_F     0.444     0    0.025   0.657     1.699  100.000   90.794
LGA    V    19_F      V    19_F     0.358     0    0.036   0.087     0.524   97.619   98.639
LGA    K    20_F      K    20_F     0.304     0    0.025   1.238     5.865  100.000   75.608
LGA    D    21_F      D    21_F     0.145     0    0.018   0.560     1.564  100.000   95.417
LGA    T    22_F      T    22_F     0.514     0    0.161   1.139     2.426   90.595   84.354
LGA    L    23_F      L    23_F     0.415     0    0.144   1.068     2.789  100.000   90.060
LGA    G    24_F      G    24_F     0.454     0    0.094   0.094     0.891   95.238   95.238
LGA    S    25_F      S    25_F     0.596     0    0.071   0.656     3.378   92.857   85.317
LGA    D    26_F      D    26_F     1.130     0    0.547   1.195     5.281   85.952   69.702
LGA    A    27_F      A    27_F     1.639     0    0.186   0.239     2.140   70.833   71.238
LGA    V    28_F      V    28_F     1.047     0    0.052   0.117     1.230   85.952   85.306
LGA    I    29_F      I    29_F     0.816     0    0.012   0.618     2.924   90.476   86.310
LGA    M    30_F      M    30_F     0.902     0    0.039   0.630     1.643   88.214   86.012
LGA    S    31_F      S    31_F     0.790     0    0.048   0.760     3.647   88.214   79.603
LGA    N    32_F      N    32_F     1.099     0    0.448   0.579     2.567   77.619   76.369
LGA    K    33_F      K    33_F     0.630     0    0.103   1.042     3.562   92.857   80.476
LGA    K    34_F      K    34_F     0.844     0    0.077   0.758     2.933   90.595   81.111
LGA    V    35_F      V    35_F     1.019     0    0.055   1.204     2.866   85.952   78.367
LGA    N    36_F      N    36_F     1.104     0    0.068   1.155     5.777   85.952   63.333
LGA    G    37_F      G    37_F     0.442     0    0.226   0.226     1.077   90.595   90.595
LGA    G    38_F      G    38_F     0.631     0    0.082   0.082     0.631   92.857   92.857
LGA    I    39_F      I    39_F     0.482     0    0.059   0.205     1.158   92.857   91.726
LGA    E    40_F      E    40_F     0.583     0    0.083   0.263     1.031   88.214   88.466
LGA    I    41_F      I    41_F     0.816     0    0.068   1.333     3.527   90.476   80.119
LGA    V    42_F      V    42_F     0.347     0    0.053   1.075     2.530   97.619   87.483
LGA    A    43_F      A    43_F     0.708     0    0.074   0.081     0.838   90.476   90.476
LGA    A    44_F      A    44_F     0.725     0    0.041   0.044     0.777   90.476   90.476
LGA    V    45_F      V    45_F     0.722     0    0.050   1.281     3.842   92.857   80.136
LGA    L    46_F      L    46_F     1.032     0    0.624   1.050     4.737   72.024   59.107
LGA    E    47_F      E    47_F     1.945     0    0.288   0.720     5.606   62.143   50.159
LGA    H    48_F      H    48_F     4.416     0    0.300   0.911    12.655   48.571   20.905
LGA    H    49_F      H    49_F     2.711     0    0.219   1.096     5.187   44.405   53.619

# 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):     1.460          1.506                  2.526           86.985   78.860

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     48    1.17    93.367    96.402     3.779

LGA_LOCAL      RMSD:   1.170  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.488  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.460  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.759960 * X  +   0.624041 * Y  +  -0.181750 * Z  +  54.816803
  Y_new =  -0.095007 * X  +  -0.383277 * Y  +  -0.918734 * Z  + -84.354660
  Z_new =  -0.642989 * X  +  -0.680934 * Y  +   0.350564 * Z  +  -5.939667 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.017222  0.698394 -1.095357   [DEG: -172.8741   40.0150  -62.7593 ]
ZXZ: -0.195304  1.212623 -2.384848   [DEG:  -11.1901   69.4782 -136.6417 ]
 
# END of job
