
#######################################################
#                                                     #
#                        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        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.70     0.70
  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     16   37   38   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     18   37   38   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     18   37   38   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     18   37   38   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     14   37   38   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     18   37   38   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     19   37   38   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     18   37   38   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     18   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     17   37   38   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     19   37   38   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     19   37   38   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     11   28   38   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     19   37   38   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     14   37   38   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     14   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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     19   37   38   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      3   37   38   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      0    3    3   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     19     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  48.72  94.87  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
GDT RMS_LOCAL    0.28   0.61   0.64   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70
GDT RMS_ALL_AT   0.96   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70

# Checking swapping
#   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     0.721     0    0.079   0.487     1.331   90.476   88.214
LGA    K     2_A      K     2_A     0.710     0    0.015   0.903     4.771   90.476   71.640
LGA    L     3_A      L     3_A     0.676     0    0.082   1.406     3.448   90.476   78.036
LGA    W     4_A      W     4_A     0.741     0    0.022   0.068     1.160   90.476   88.537
LGA    I     5_A      I     5_A     1.124     0    0.084   1.335     4.816   88.214   73.333
LGA    L     6_A      L     6_A     0.622     0    0.041   1.387     3.195   95.238   81.429
LGA    Q     7_A      Q     7_A     0.269     0    0.028   1.419     5.387  100.000   73.757
LGA    K     8_A      K     8_A     0.471     0    0.035   0.162     0.823  100.000   94.709
LGA    I     9_A      I     9_A     0.316     0    0.020   0.096     1.291  100.000   95.298
LGA    Y    10_A      Y    10_A     0.345     0    0.021   0.072     1.422   97.619   92.143
LGA    E    11_A      E    11_A     0.449     0    0.024   0.090     0.887  100.000   94.709
LGA    I    12_A      I    12_A     0.280     0    0.050   0.797     1.898   97.619   88.631
LGA    M    13_A      M    13_A     0.493     0    0.010   0.118     1.003   95.238   91.726
LGA    V    14_A      V    14_A     0.681     0    0.025   0.024     0.930   90.476   90.476
LGA    R    15_A      R    15_A     0.465     0    0.021   1.346     5.916   97.619   73.810
LGA    L    16_A      L    16_A     0.402     0    0.010   0.080     0.648   95.238   97.619
LGA    D    17_A      D    17_A     0.770     0    0.017   0.899     2.990   90.476   77.798
LGA    E    18_A      E    18_A     0.465     0    0.030   0.175     2.237  100.000   86.931
LGA    E    19_A      E    19_A     0.629     0    0.103   0.135     1.970   90.595   82.646
LGA    G    20_A      G    20_A     1.283     0    0.056   0.056     1.833   81.548   81.548
LGA    H    21_A      H    21_A     0.551     0    0.027   0.200     0.769   90.476   90.476
LGA    G    22_A      G    22_A     0.954     0    0.082   0.082     0.954   90.476   90.476
LGA    E    23_A      E    23_A     0.877     0    0.041   0.642     1.483   90.476   87.460
LGA    A    24_A      A    24_A     0.360     0    0.036   0.033     0.426  100.000  100.000
LGA    S    25_A      S    25_A     0.181     0    0.018   0.075     0.671  100.000   98.413
LGA    L    26_A      L    26_A     0.559     0    0.031   0.043     1.007   92.857   90.536
LGA    M    27_A      M    27_A     0.669     0    0.059   1.207     5.225   90.476   70.714
LGA    V    28_A      V    28_A     0.436     0    0.035   0.110     0.565  100.000   98.639
LGA    S    29_A      S    29_A     0.458     0    0.025   0.043     0.593   95.238   95.238
LGA    D    30_A      D    30_A     0.577     0    0.032   0.105     0.806   90.476   90.476
LGA    L    31_A      L    31_A     0.683     0    0.012   1.409     3.847   90.476   79.167
LGA    I    32_A      I    32_A     0.561     0    0.027   0.085     0.724   90.476   94.048
LGA    Y    33_A      Y    33_A     0.737     0    0.087   1.447     9.974   90.476   52.063
LGA    E    34_A      E    34_A     0.852     0    0.020   0.764     3.603   90.476   76.561
LGA    F    35_A      F    35_A     0.739     0    0.018   1.048     4.066   90.476   75.152
LGA    M    36_A      M    36_A     0.509     0    0.093   0.143     2.086   97.619   89.702
LGA    K    37_A      K    37_A     0.300     0    0.072   1.043     4.600   95.238   78.677
LGA    R    38_A      R    38_A     0.792     0    0.617   0.992     4.744   84.524   74.416
LGA    D    39_A      D    39_A     1.857     3    0.324   0.449     2.624   75.000   44.643

# 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):     0.699          0.711                  1.748           93.001   84.099

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.70    98.718    99.404     4.880

LGA_LOCAL      RMSD:   0.699  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.699  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.699  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.324487 * X  +  -0.939272 * Y  +  -0.111696 * Z  + -19.257261
  Y_new =   0.604589 * X  +   0.296768 * Y  +  -0.739190 * Z  +   0.506076
  Z_new =   0.727448 * X  +   0.172327 * Y  +   0.664171 * Z  + -19.476189 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.078216 -0.814595  0.253865   [DEG:   61.7772  -46.6729   14.5454 ]
ZXZ: -0.149971  0.844412  1.338191   [DEG:   -8.5927   48.3812   76.6727 ]
 
# END of job
