
#######################################################
#                                                     #
#                        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     17   35   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     17   35   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     17   35   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   35   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     11   33   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     17   35   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     21   35   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     17   35   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     21   35   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     17   35   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     18   35   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     18   35   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     17   35   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     17   34   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     17   35   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     21   35   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     17   35   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     17   35   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      8   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     21   35   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     20   35   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     12   30   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      0    3   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     21     35     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  53.85  89.74 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.61   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   0.69
GDT RMS_ALL_AT   0.81   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   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     0.711     0    0.255   0.936     1.945   83.810   82.738
LGA    K     2_A      K     2_A     0.958     0    0.038   0.201     2.090   90.476   84.603
LGA    L     3_A      L     3_A     0.710     0    0.068   1.336     3.901   92.857   78.393
LGA    W     4_A      W     4_A     0.386     0    0.051   0.317     2.510   95.238   82.585
LGA    I     5_A      I     5_A     1.091     0    0.084   1.366     5.135   88.214   72.738
LGA    L     6_A      L     6_A     0.730     0    0.021   1.388     3.035   95.238   83.452
LGA    Q     7_A      Q     7_A     0.378     0    0.056   1.401     5.020  100.000   73.810
LGA    K     8_A      K     8_A     0.524     0    0.043   0.292     1.770   97.619   87.725
LGA    I     9_A      I     9_A     0.227     0    0.016   0.139     1.217  100.000   95.298
LGA    Y    10_A      Y    10_A     0.816     0    0.013   1.062     5.334   88.214   68.849
LGA    E    11_A      E    11_A     1.038     0    0.030   0.087     2.236   85.952   78.730
LGA    I    12_A      I    12_A     0.489     0    0.045   0.808     2.137   95.238   86.429
LGA    M    13_A      M    13_A     0.607     0    0.016   0.201     1.139   92.857   90.536
LGA    V    14_A      V    14_A     1.098     0    0.035   0.049     1.637   88.214   82.857
LGA    R    15_A      R    15_A     0.952     0    0.020   0.531     1.675   90.476   83.939
LGA    L    16_A      L    16_A     0.285     0    0.026   0.054     0.475  100.000  100.000
LGA    D    17_A      D    17_A     0.638     0    0.031   0.231     0.985   92.857   91.667
LGA    E    18_A      E    18_A     0.909     0    0.031   0.148     2.911   90.476   77.249
LGA    E    19_A      E    19_A     0.856     0    0.111   0.216     2.538   88.214   77.090
LGA    G    20_A      G    20_A     0.965     0    0.021   0.021     1.538   83.810   83.810
LGA    H    21_A      H    21_A     0.660     0    0.066   0.233     1.401   90.476   87.762
LGA    G    22_A      G    22_A     0.670     0    0.031   0.031     0.670   90.476   90.476
LGA    E    23_A      E    23_A     0.582     0    0.027   0.619     1.520   95.238   89.630
LGA    A    24_A      A    24_A     0.395     0    0.032   0.043     0.491  100.000  100.000
LGA    S    25_A      S    25_A     0.450     0    0.023   0.045     0.597  100.000   98.413
LGA    L    26_A      L    26_A     0.377     0    0.065   0.066     0.672  100.000   96.429
LGA    M    27_A      M    27_A     0.198     0    0.018   0.179     0.633  100.000   98.810
LGA    V    28_A      V    28_A     0.117     0    0.033   0.113     0.405  100.000  100.000
LGA    S    29_A      S    29_A     0.381     0    0.006   0.709     2.111  100.000   94.127
LGA    D    30_A      D    30_A     0.328     0    0.023   0.068     0.660  100.000   97.619
LGA    L    31_A      L    31_A     0.345     0    0.015   0.325     1.678   97.619   93.036
LGA    I    32_A      I    32_A     0.499     0    0.025   0.117     0.739   95.238   96.429
LGA    Y    33_A      Y    33_A     0.494     0    0.011   0.220     1.622   97.619   90.714
LGA    E    34_A      E    34_A     0.446     0    0.024   1.140     4.626   95.238   78.571
LGA    F    35_A      F    35_A     0.372     0    0.032   0.481     1.135  100.000   94.892
LGA    M    36_A      M    36_A     0.457     0    0.098   0.231     2.225   95.238   88.512
LGA    K    37_A      K    37_A     0.853     0    0.028   1.046     5.752   88.214   72.804
LGA    R    38_A      R    38_A     1.291     0    0.647   1.172     5.330   69.762   63.593
LGA    D    39_A      D    39_A     1.194     3    0.134   0.146     5.458   59.762   35.298

# 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):     0.693          0.887                  1.460           92.683   85.375

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.69    97.436    99.190     4.919

LGA_LOCAL      RMSD:   0.693  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.693  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.693  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.564830 * X  +  -0.026227 * Y  +  -0.824791 * Z  + -35.344372
  Y_new =  -0.813235 * X  +  -0.187327 * Y  +  -0.550960 * Z  +   3.988974
  Z_new =  -0.140056 * X  +   0.981947 * Y  +  -0.127136 * Z  + -13.329894 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.963740  0.140518  1.699554   [DEG:  -55.2182    8.0511   97.3773 ]
ZXZ: -0.981871  1.698278 -0.141675   [DEG:  -56.2571   97.3041   -8.1174 ]
 
# END of job
