
#######################################################
#                                                     #
#                        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        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.69     0.69
  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     18   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     15   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     21   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     20   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     21   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     21   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     21   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     21   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     21   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     21   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     21   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     18   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     21   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     20   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      8   29   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     20   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     15   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     15   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     21   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     21   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     21   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     21   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     21   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     21   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     21   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     21   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     21   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     20   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     20   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     21   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     21   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     21   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     21   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   24   37   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     21     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  53.85  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    0.35   0.59   0.61   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   0.77   0.69   0.70   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  E    11_A      E    11_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     0.845     0    0.086   0.488     1.415   88.214   87.083
LGA    K     2_A      K     2_A     0.757     0    0.020   0.803     3.686   90.476   75.926
LGA    L     3_A      L     3_A     0.540     0    0.092   1.402     3.397   90.476   78.333
LGA    W     4_A      W     4_A     0.642     0    0.020   0.060     1.104   90.476   88.537
LGA    I     5_A      I     5_A     1.000     0    0.082   1.335     4.678   90.595   75.595
LGA    L     6_A      L     6_A     0.582     0    0.039   1.394     3.269   95.238   81.429
LGA    Q     7_A      Q     7_A     0.187     0    0.019   1.410     5.288  100.000   73.757
LGA    K     8_A      K     8_A     0.421     0    0.028   0.160     0.854  100.000   95.767
LGA    I     9_A      I     9_A     0.348     0    0.025   0.096     1.286  100.000   95.298
LGA    Y    10_A      Y    10_A     0.362     0    0.027   0.075     1.344   97.619   92.143
LGA    E    11_A      E    11_A     0.456     0    0.041   0.791     2.968  100.000   79.894
LGA    I    12_A      I    12_A     0.255     0    0.051   0.791     1.820   97.619   88.631
LGA    M    13_A      M    13_A     0.475     0    0.008   0.118     0.958   95.238   92.857
LGA    V    14_A      V    14_A     0.644     0    0.023   0.027     0.898   90.476   90.476
LGA    R    15_A      R    15_A     0.469     0    0.010   1.206     5.509   97.619   72.121
LGA    L    16_A      L    16_A     0.441     0    0.007   0.055     0.683   95.238   95.238
LGA    D    17_A      D    17_A     0.803     0    0.018   0.901     2.941   90.476   77.798
LGA    E    18_A      E    18_A     0.532     0    0.035   0.156     2.460   95.238   83.915
LGA    E    19_A      E    19_A     0.642     0    0.097   0.159     1.934   90.595   83.651
LGA    G    20_A      G    20_A     1.298     0    0.051   0.051     1.819   81.548   81.548
LGA    H    21_A      H    21_A     0.527     0    0.026   0.206     0.714   92.857   91.429
LGA    G    22_A      G    22_A     0.933     0    0.083   0.083     0.933   90.476   90.476
LGA    E    23_A      E    23_A     0.854     0    0.036   0.648     1.576   90.476   86.508
LGA    A    24_A      A    24_A     0.340     0    0.043   0.043     0.391  100.000  100.000
LGA    S    25_A      S    25_A     0.153     0    0.022   0.072     0.643  100.000   98.413
LGA    L    26_A      L    26_A     0.503     0    0.028   0.038     0.926   92.857   91.667
LGA    M    27_A      M    27_A     0.596     0    0.025   0.776     1.967   90.476   86.012
LGA    V    28_A      V    28_A     0.439     0    0.040   0.104     0.563   97.619   97.279
LGA    S    29_A      S    29_A     0.497     0    0.028   0.047     0.648   95.238   95.238
LGA    D    30_A      D    30_A     0.591     0    0.025   0.102     0.781   90.476   90.476
LGA    L    31_A      L    31_A     0.702     0    0.005   1.404     3.750   90.476   79.167
LGA    I    32_A      I    32_A     0.608     0    0.027   0.087     0.829   90.476   94.048
LGA    Y    33_A      Y    33_A     0.840     0    0.078   1.465    10.112   90.476   50.873
LGA    E    34_A      E    34_A     0.922     0    0.035   0.543     3.358   90.476   78.254
LGA    F    35_A      F    35_A     0.672     0    0.016   1.111     4.459   95.238   74.805
LGA    M    36_A      M    36_A     0.241     0    0.087   0.140     1.853  100.000   93.095
LGA    K    37_A      K    37_A     0.257     0    0.081   1.027     4.648   95.238   81.587
LGA    R    38_A      R    38_A     0.464     0    0.683   1.262     5.990   86.905   68.398
LGA    D    39_A      D    39_A     1.927     3    0.358   0.486     2.626   68.929   41.607

# 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):     0.688          0.720                  1.747           92.970   84.085

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.69    98.718    99.404     4.946

LGA_LOCAL      RMSD:   0.688  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.688  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.688  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.309449 * X  +  -0.940010 * Y  +   0.143603 * Z  + -19.474586
  Y_new =   0.512030 * X  +   0.037462 * Y  +  -0.858150 * Z  +   0.923388
  Z_new =   0.801291 * X  +   0.339082 * Y  +   0.492906 * Z  + -20.839844 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.027180 -0.929449  0.602576   [DEG:   58.8531  -53.2535   34.5250 ]
ZXZ:  0.165804  1.055370  1.170477   [DEG:    9.4998   60.4682   67.0634 ]
 
# END of job
