
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   39 , 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:    39       1_A - 39_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     D     1_A     D     1_A     39   39   39     12   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     39   39   39     21   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     39   39   39     22   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     39   39   39     12   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     39   39   39     14   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     39   39   39      4   33   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     39   39   39      3   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     24     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  61.54  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.58   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61
GDT RMS_ALL_AT   0.70   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  Y    10_A      Y    10_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  Y    33_A      Y    33_A
#   possible swapping detected:  F    35_A      F    35_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.896     0    0.326   0.914     1.897   81.548   79.345
LGA    K     2_A      K     2_A     0.970     0    0.034   0.174     1.756   90.476   85.503
LGA    L     3_A      L     3_A     0.797     0    0.075   1.382     3.657   90.476   75.357
LGA    W     4_A      W     4_A     0.490     0    0.036   0.108     1.719   95.238   88.061
LGA    I     5_A      I     5_A     1.010     0    0.076   1.363     5.131   90.595   75.000
LGA    L     6_A      L     6_A     0.587     0    0.024   1.377     2.980   95.238   84.345
LGA    Q     7_A      Q     7_A     0.237     0    0.048   1.415     4.978  100.000   75.926
LGA    K     8_A      K     8_A     0.545     0    0.046   0.180     0.928   97.619   93.651
LGA    I     9_A      I     9_A     0.186     0    0.017   0.098     0.890  100.000   97.619
LGA    Y    10_A      Y    10_A     0.568     0    0.011   0.076     1.538   92.857   87.540
LGA    E    11_A      E    11_A     0.898     0    0.018   0.137     1.981   88.214   81.587
LGA    I    12_A      I    12_A     0.516     0    0.038   0.800     2.112   92.857   85.238
LGA    M    13_A      M    13_A     0.443     0    0.015   0.181     1.009   95.238   92.917
LGA    V    14_A      V    14_A     0.876     0    0.035   0.046     1.323   90.476   86.599
LGA    R    15_A      R    15_A     0.867     0    0.019   0.891     5.020   90.476   73.853
LGA    L    16_A      L    16_A     0.297     0    0.023   0.040     0.541  100.000   98.810
LGA    D    17_A      D    17_A     0.463     0    0.041   0.223     0.883  100.000   95.238
LGA    E    18_A      E    18_A     0.740     0    0.030   0.123     2.466   90.476   78.942
LGA    E    19_A      E    19_A     0.738     0    0.106   0.231     2.347   88.214   78.836
LGA    G    20_A      G    20_A     0.804     0    0.031   0.031     1.349   90.595   90.595
LGA    H    21_A      H    21_A     0.526     0    0.079   0.225     1.324   92.857   89.667
LGA    G    22_A      G    22_A     0.517     0    0.027   0.027     0.535   92.857   92.857
LGA    E    23_A      E    23_A     0.570     0    0.023   0.685     2.211   95.238   87.831
LGA    A    24_A      A    24_A     0.372     0    0.031   0.042     0.485  100.000  100.000
LGA    S    25_A      S    25_A     0.333     0    0.038   0.058     0.395  100.000  100.000
LGA    L    26_A      L    26_A     0.396     0    0.057   0.053     0.681  100.000   96.429
LGA    M    27_A      M    27_A     0.273     0    0.021   0.150     0.628  100.000   98.810
LGA    V    28_A      V    28_A     0.160     0    0.028   0.096     0.315  100.000  100.000
LGA    S    29_A      S    29_A     0.427     0    0.003   0.011     0.673  100.000   96.825
LGA    D    30_A      D    30_A     0.306     0    0.019   0.068     0.712  100.000   96.429
LGA    L    31_A      L    31_A     0.200     0    0.015   0.132     1.004   97.619   94.107
LGA    I    32_A      I    32_A     0.370     0    0.023   0.091     0.579   97.619   97.619
LGA    Y    33_A      Y    33_A     0.354     0    0.015   0.234     1.528  100.000   92.262
LGA    E    34_A      E    34_A     0.352     0    0.023   1.141     4.633   97.619   78.783
LGA    F    35_A      F    35_A     0.290     0    0.032   0.537     1.225  100.000   94.069
LGA    M    36_A      M    36_A     0.331     0    0.087   0.715     2.392   95.238   87.440
LGA    K    37_A      K    37_A     0.783     0    0.037   1.064     5.818   90.595   73.862
LGA    R    38_A      R    38_A     1.218     0    0.209   1.280     6.249   77.262   62.944
LGA    D    39_A      D    39_A     0.736     3    0.214   0.221     2.711   77.738   46.964

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     326    326  100.00                39
SUMMARY(RMSD_GDC):     0.608          0.678                  1.353           94.237   86.971

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.61    99.359    99.798     5.505

LGA_LOCAL      RMSD:   0.608  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.608  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.608  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.635940 * X  +  -0.362269 * Y  +   0.681426 * Z  + -35.099289
  Y_new =   0.684001 * X  +  -0.673479 * Y  +   0.280301 * Z  +   5.878405
  Z_new =   0.357382 * X  +   0.644351 * Y  +   0.676085 * Z  + -13.629146 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.319799 -0.365463  0.761370   [DEG:  132.9147  -20.9395   43.6233 ]
ZXZ:  1.961044  0.828361  0.506398   [DEG:  112.3595   47.4616   29.0144 ]
 
# END of job
