
#######################################################
#                                                     #
#                        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   41 (  336),  selected   39 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       4_B - 42_B        2.49     2.49
  LCS_AVERAGE:     95.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       4_B - 39_B        1.65     2.60
  LCS_AVERAGE:     85.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       4_B - 33_B        0.96     2.98
  LCS_AVERAGE:     64.48

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     Q     4_B     Q     4_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     R     5_B     R     5_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_B     L     6_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     F     7_B     F     7_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     V     8_B     V     8_B     30   36   39      6   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     9_B     L     9_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    10_B     D    10_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    11_B     N    11_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    12_B     E    12_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    13_B     R    13_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    14_B     Y    14_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    15_B     D    15_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    16_B     S    16_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    17_B     F    17_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    18_B     I    18_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     T    19_B     T    19_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    20_B     Q    20_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    21_B     L    21_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    22_B     E    22_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    23_B     A    23_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    24_B     P    24_B     30   36   39     20   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    25_B     V    25_B     30   36   39      3   23   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    26_B     Q    26_B     30   36   39      9   14   15   17   31   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    27_B     N    27_B     30   36   39      9   14   24   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    28_B     A    28_B     30   36   39      9   14   28   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    29_B     E    29_B     30   36   39      9   13   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    30_B     G    30_B     30   36   39      9   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    31_B     R    31_B     30   36   39      9   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    32_B     E    32_B     30   36   39     18   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    33_B     R    33_B     30   36   39     18   25   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    34_B     L    34_B     16   36   39      9   14   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    35_B     M    35_B     16   36   39      9   18   29   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    36_B     A    36_B     16   36   39      9   14   28   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    37_B     V    37_B     16   36   39      9   14   17   31   33   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    38_B     K    38_B     16   36   39      9   14   15   19   32   34   35   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    39_B     P    39_B     16   36   39      4   14   15   16   17   21   33   36   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    40_B     E    40_B     16   23   39      4    5   13   16   17   18   20   23   28   34   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     W    41_B     W    41_B     16   22   39      4   14   15   16   17   19   21   26   37   37   38   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    42_B     K    42_B      3   19   39      3    3    3    3    4    4   15   17   28   34   38   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  81.55  (  64.48   85.05   95.12 )

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     20     25     29     31     33     34     35     36     37     37     38     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  48.78  60.98  70.73  75.61  80.49  82.93  85.37  87.80  90.24  90.24  92.68  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12
GDT RMS_LOCAL    0.31   0.51   0.75   0.91   1.09   1.21   1.38   1.65   1.99   1.99   2.24   2.49   2.49   2.49   2.49   2.49   2.49   2.49   2.49   2.49
GDT RMS_ALL_AT   2.94   2.84   2.80   2.85   2.73   2.76   2.68   2.60   2.53   2.53   2.51   2.49   2.49   2.49   2.49   2.49   2.49   2.49   2.49   2.49

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q     4_B      Q     4_B     1.190     0    0.041   0.210     1.339   81.429   81.429
LGA    R     5_B      R     5_B     0.858     0    0.107   0.372     1.822   90.476   83.983
LGA    L     6_B      L     6_B     0.739     0    0.058   0.087     1.246   88.214   88.214
LGA    F     7_B      F     7_B     0.556     0    0.016   0.111     0.823   90.476   93.074
LGA    V     8_B      V     8_B     1.017     0    0.025   1.161     2.470   88.214   80.544
LGA    L     9_B      L     9_B     0.770     0    0.028   0.124     0.980   90.476   90.476
LGA    D    10_B      D    10_B     0.950     0    0.045   0.424     1.729   88.214   82.679
LGA    N    11_B      N    11_B     0.678     0    0.075   0.835     2.868   88.214   81.845
LGA    E    12_B      E    12_B     0.834     0    0.052   1.162     6.207   90.476   67.196
LGA    R    13_B      R    13_B     1.053     0    0.025   1.086     3.576   85.952   72.251
LGA    Y    14_B      Y    14_B     0.667     0    0.047   0.139     1.068   92.857   90.556
LGA    D    15_B      D    15_B     0.353     0    0.032   0.451     1.222   97.619   95.298
LGA    S    16_B      S    16_B     0.597     0    0.022   0.772     2.449   92.857   87.778
LGA    F    17_B      F    17_B     0.517     0    0.023   0.257     0.916   90.476   90.476
LGA    I    18_B      I    18_B     0.515     0    0.028   0.111     0.653   92.857   91.667
LGA    T    19_B      T    19_B     0.459     0    0.022   0.280     1.251   97.619   94.626
LGA    Q    20_B      Q    20_B     0.459     0    0.028   0.964     3.323  100.000   86.455
LGA    L    21_B      L    21_B     0.503     0    0.031   0.257     1.457   92.857   90.595
LGA    E    22_B      E    22_B     0.579     0    0.019   0.728     2.270   92.857   80.106
LGA    A    23_B      A    23_B     0.760     0    0.095   0.114     1.167   88.214   88.667
LGA    P    24_B      P    24_B     0.702     0    0.075   0.314     1.615   83.810   89.388
LGA    V    25_B      V    25_B     1.557     0    0.182   1.253     3.949   75.000   71.088
LGA    Q    26_B      Q    26_B     3.472     0    0.634   1.178     8.124   42.976   31.958
LGA    N    27_B      N    27_B     2.553     0    0.186   0.198     3.237   62.857   59.107
LGA    A    28_B      A    28_B     2.344     0    0.099   0.110     2.637   69.048   66.667
LGA    E    29_B      E    29_B     1.782     0    0.063   0.499     2.813   77.381   70.423
LGA    G    30_B      G    30_B     1.379     0    0.069   0.069     1.500   79.286   79.286
LGA    R    31_B      R    31_B     1.211     0    0.052   1.169     7.652   88.333   59.004
LGA    E    32_B      E    32_B     0.423     0    0.082   0.780     3.719   95.238   79.471
LGA    R    33_B      R    33_B     0.277     0    0.050   1.349     5.205   92.976   74.113
LGA    L    34_B      L    34_B     1.372     0    0.023   0.055     2.556   81.548   72.262
LGA    M    35_B      M    35_B     1.106     0    0.016   0.590     2.974   81.548   80.714
LGA    A    36_B      A    36_B     1.506     0    0.011   0.017     2.236   72.976   74.667
LGA    V    37_B      V    37_B     2.355     0    0.047   0.061     2.888   62.976   62.653
LGA    K    38_B      K    38_B     3.597     4    0.126   0.145     5.846   36.548   20.370
LGA    P    39_B      P    39_B     5.462     0    0.081   0.366     6.065   25.476   31.633
LGA    E    40_B      E    40_B     7.874     0    0.365   0.942    11.287    8.571    4.021
LGA    W    41_B      W    41_B     7.155     0    0.536   0.902     8.826    8.214   11.259
LGA    K    42_B      K    42_B     7.155     0    0.039   0.929    13.672   21.667    9.947

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     325    325  100.00                41
SUMMARY(RMSD_GDC):     2.491          2.483                  3.225           72.848   67.462

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   41    4.0     36    1.65    79.878    83.523     2.054

LGA_LOCAL      RMSD:   1.653  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.595  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   2.491  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.245136 * X  +  -0.951399 * Y  +   0.186406 * Z  +  16.160995
  Y_new =  -0.382528 * X  +   0.271591 * Y  +   0.883126 * Z  + -30.361153
  Z_new =  -0.890832 * X  +   0.145180 * Y  +  -0.430513 * Z  +  21.832195 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.140700  1.099172  2.816343   [DEG: -122.6531   62.9779  161.3646 ]
ZXZ:  2.933570  2.015858 -1.409245   [DEG:  168.0812  115.5002  -80.7438 ]
 
# END of job
