
#######################################################
#                                                     #
#                        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     15   36   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   36   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   36   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     20   36   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   36   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   36   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     22   36   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     20   36   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     22   36   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     20   36   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     17   36   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     22   36   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     22   36   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   36   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   36   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     22   36   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     21   36   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   36   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     14   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     22   36   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     16   34   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     11   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      4   35   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     22     36     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  56.41  92.31 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.63   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   0.69
GDT RMS_ALL_AT   0.79   0.73   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   0.69

# 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     1.062     0    0.280   0.919     1.711   79.286   80.476
LGA    K     2_A      K     2_A     1.145     0    0.032   0.147     1.784   81.429   80.476
LGA    L     3_A      L     3_A     0.904     0    0.073   1.381     3.657   88.214   74.226
LGA    W     4_A      W     4_A     0.611     0    0.034   0.126     2.033   90.476   82.925
LGA    I     5_A      I     5_A     1.174     0    0.074   1.371     5.178   88.214   72.738
LGA    L     6_A      L     6_A     0.781     0    0.022   1.396     3.064   92.857   81.131
LGA    Q     7_A      Q     7_A     0.230     0    0.043   1.398     4.942  100.000   75.291
LGA    K     8_A      K     8_A     0.574     0    0.047   0.176     1.121   97.619   89.630
LGA    I     9_A      I     9_A     0.276     0    0.023   0.139     1.210  100.000   95.298
LGA    Y    10_A      Y    10_A     0.693     0    0.013   0.054     1.867   92.857   85.317
LGA    E    11_A      E    11_A     0.996     0    0.022   0.142     2.260   88.214   79.735
LGA    I    12_A      I    12_A     0.520     0    0.046   0.805     2.245   92.857   84.048
LGA    M    13_A      M    13_A     0.467     0    0.014   0.196     1.291   95.238   91.726
LGA    V    14_A      V    14_A     1.028     0    0.038   0.050     1.606   88.214   84.082
LGA    R    15_A      R    15_A     1.015     0    0.018   0.910     4.896   88.214   73.506
LGA    L    16_A      L    16_A     0.332     0    0.022   0.057     0.595  100.000   98.810
LGA    D    17_A      D    17_A     0.576     0    0.045   0.203     0.989   95.238   92.857
LGA    E    18_A      E    18_A     0.964     0    0.028   0.122     2.835   90.476   78.095
LGA    E    19_A      E    19_A     0.847     0    0.101   0.193     2.436   88.214   77.937
LGA    G    20_A      G    20_A     0.693     0    0.033   0.033     1.286   90.595   90.595
LGA    H    21_A      H    21_A     0.512     0    0.089   0.218     1.397   95.238   90.619
LGA    G    22_A      G    22_A     0.561     0    0.021   0.021     0.619   90.476   90.476
LGA    E    23_A      E    23_A     0.637     0    0.018   0.243     1.279   90.476   89.471
LGA    A    24_A      A    24_A     0.457     0    0.021   0.032     0.561   97.619   98.095
LGA    S    25_A      S    25_A     0.397     0    0.037   0.057     0.474  100.000  100.000
LGA    L    26_A      L    26_A     0.495     0    0.056   0.053     0.786   95.238   92.857
LGA    M    27_A      M    27_A     0.316     0    0.018   0.143     0.472  100.000  100.000
LGA    V    28_A      V    28_A     0.147     0    0.029   0.124     0.355  100.000  100.000
LGA    S    29_A      S    29_A     0.436     0    0.006   0.011     0.693  100.000   96.825
LGA    D    30_A      D    30_A     0.281     0    0.021   0.057     0.774  100.000   96.429
LGA    L    31_A      L    31_A     0.220     0    0.016   0.116     1.078   97.619   94.107
LGA    I    32_A      I    32_A     0.405     0    0.020   0.100     0.651   97.619   97.619
LGA    Y    33_A      Y    33_A     0.395     0    0.011   0.211     1.362  100.000   92.976
LGA    E    34_A      E    34_A     0.433     0    0.030   1.142     4.600   95.238   77.725
LGA    F    35_A      F    35_A     0.380     0    0.013   0.507     1.277  100.000   94.892
LGA    M    36_A      M    36_A     0.354     0    0.094   0.712     2.287   95.238   87.440
LGA    K    37_A      K    37_A     0.951     0    0.033   1.068     5.791   85.952   69.788
LGA    R    38_A      R    38_A     1.308     0    0.174   1.273     5.816   77.262   64.675
LGA    D    39_A      D    39_A     0.729     3    0.108   0.099     2.353   81.786   50.000

# 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):     0.691          0.727                  1.376           93.025   85.972

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.69    98.077    99.393     4.928

LGA_LOCAL      RMSD:   0.691  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.691  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.691  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.794324 * X  +  -0.060675 * Y  +   0.604457 * Z  + -34.609428
  Y_new =  -0.108571 * X  +  -0.964801 * Y  +  -0.239521 * Z  +   6.953317
  Z_new =   0.597714 * X  +  -0.255884 * Y  +   0.759777 * Z  + -12.985237 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.005750 -0.640646 -0.324857   [DEG: -172.2168  -36.7063  -18.6129 ]
ZXZ:  1.193520  0.707826  1.975294   [DEG:   68.3836   40.5554  113.1760 ]
 
# END of job
