
#######################################################
#                                                     #
#                        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   41 (  340),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , 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:    41       2_B - 42_B        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       3_B - 25_B        0.91     2.20
  LCS_AVERAGE:     46.10

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      3   41   41      3    3    4    9   10   13   16   31   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     23   41   41      7   24   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     23   41   41      5   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     23   41   41      5   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     23   41   41      4   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     23   41   41      4   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     23   41   41     10   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     23   41   41      9   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     23   41   41      7   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     23   41   41     10   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     23   41   41     10   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     23   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     23   41   41     10   26   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     23   41   41     10   25   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     23   41   41      5   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     23   41   41      8   25   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     23   41   41     10   22   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     23   41   41      8   22   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     23   41   41      3   13   24   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     15   41   41      3    5    8   15   23   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     15   41   41      3   14   28   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     15   41   41      9   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     15   41   41      3   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     15   41   41     10   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     15   41   41      4   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     15   41   41     12   27   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     15   41   41      4   16   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     15   41   41      3   14   31   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     15   41   41      3   22   35   37   38   39   39   39   39   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      0    3    3    3    9    9   22   27   38   39   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  82.03  (  46.10  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     12     27     35     37     38     39     39     39     39     40     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  29.27  65.85  85.37  90.24  92.68  95.12  95.12  95.12  95.12  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.67   0.90   1.01   1.07   1.22   1.22   1.22   1.22   1.54   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92
GDT RMS_ALL_AT   2.16   2.10   2.01   2.00   1.99   1.97   1.97   1.97   1.97   1.95   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    32_B      E    32_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     6.206     0    0.431   0.455     6.736   19.762   20.095
LGA    S     3_B      S     3_B     1.309     0    0.164   0.546     2.386   81.786   81.746
LGA    Q     4_B      Q     4_B     0.926     0    0.064   1.046     4.559   88.214   77.090
LGA    R     5_B      R     5_B     0.650     0    0.103   0.860     2.790   90.476   79.610
LGA    L     6_B      L     6_B     0.934     0    0.066   0.106     1.678   90.476   84.881
LGA    F     7_B      F     7_B     0.897     0    0.050   0.143     1.308   85.952   88.831
LGA    V     8_B      V     8_B     0.988     0    0.042   1.157     2.841   90.476   82.041
LGA    L     9_B      L     9_B     0.855     0    0.024   0.229     1.571   90.476   87.143
LGA    D    10_B      D    10_B     1.132     0    0.059   0.182     1.521   85.952   83.750
LGA    N    11_B      N    11_B     0.669     0    0.074   0.933     3.300   92.857   81.190
LGA    E    12_B      E    12_B     0.453     0    0.079   1.567     6.759   95.238   66.349
LGA    R    13_B      R    13_B     0.839     0    0.058   1.070     3.552   88.214   73.896
LGA    Y    14_B      Y    14_B     0.552     0    0.033   0.262     1.086   95.238   91.310
LGA    D    15_B      D    15_B     0.338     0    0.012   0.349     0.783   97.619   96.429
LGA    S    16_B      S    16_B     0.998     0    0.043   0.305     1.230   85.952   85.952
LGA    F    17_B      F    17_B     0.800     0    0.027   0.165     1.248   90.476   87.186
LGA    I    18_B      I    18_B     0.058     0    0.021   0.751     3.201  100.000   92.560
LGA    T    19_B      T    19_B     0.916     0    0.052   0.887     2.853   88.214   80.612
LGA    Q    20_B      Q    20_B     1.322     0    0.025   1.162     3.299   85.952   78.095
LGA    L    21_B      L    21_B     0.817     0    0.033   0.591     1.176   90.476   88.274
LGA    E    22_B      E    22_B     1.022     0    0.014   0.720     1.564   81.548   83.545
LGA    A    23_B      A    23_B     1.244     0    0.120   0.146     1.489   83.690   83.238
LGA    P    24_B      P    24_B     1.396     0    0.021   0.196     1.902   77.143   75.306
LGA    V    25_B      V    25_B     2.197     0    0.179   1.253     3.719   64.881   64.082
LGA    Q    26_B      Q    26_B     3.801     0    0.462   0.640     5.752   40.714   33.915
LGA    N    27_B      N    27_B     2.118     0    0.141   0.142     2.742   70.952   65.952
LGA    A    28_B      A    28_B     0.693     0    0.074   0.080     1.260   88.214   86.857
LGA    E    29_B      E    29_B     1.330     0    0.104   0.547     3.781   85.952   69.365
LGA    G    30_B      G    30_B     0.678     0    0.058   0.058     0.936   92.857   92.857
LGA    R    31_B      R    31_B     0.735     0    0.039   1.234     5.967   90.476   65.714
LGA    E    32_B      E    32_B     0.794     0    0.079   1.135     6.005   88.214   68.730
LGA    R    33_B      R    33_B     0.412     0    0.063   0.635     1.804   92.857   86.537
LGA    L    34_B      L    34_B     0.641     0    0.023   0.095     1.065   90.595   90.536
LGA    M    35_B      M    35_B     1.029     0    0.082   0.474     1.706   83.690   80.417
LGA    A    36_B      A    36_B     0.904     0    0.036   0.034     1.181   95.238   92.476
LGA    V    37_B      V    37_B     0.755     0    0.657   1.332     3.859   78.810   77.551
LGA    K    38_B      K    38_B     0.599     4    0.122   0.119     1.079   88.214   49.259
LGA    P    39_B      P    39_B     1.347     0    0.044   0.199     1.516   79.286   80.204
LGA    E    40_B      E    40_B     1.968     0    0.277   0.271     7.277   81.667   51.217
LGA    W    41_B      W    41_B     1.551     0    0.566   0.891     3.981   60.238   76.667
LGA    K    42_B      K    42_B     7.947     0    0.081   1.185    14.274    7.857    3.492

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     1.924          1.997                  2.655           81.876   75.243

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   41   41    4.0     39    1.22    87.805    93.870     2.956

LGA_LOCAL      RMSD:   1.219  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.973  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.924  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.521715 * X  +  -0.468611 * Y  +  -0.712894 * Z  +  25.237505
  Y_new =   0.803159 * X  +   0.011973 * Y  +  -0.595644 * Z  + -24.699697
  Z_new =   0.287660 * X  +  -0.883324 * Y  +   0.370123 * Z  +  11.714415 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.146875 -0.291783 -1.174009   [DEG:  123.0069  -16.7179  -67.2658 ]
ZXZ: -0.874763  1.191655  2.826767   [DEG:  -50.1203   68.2768  161.9618 ]
 
# END of job
