
#######################################################
#                                                     #
#                        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   42 (  348),  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:    40       2_B - 41_B        4.90     5.29
  LCS_AVERAGE:     97.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_B - 34_B        1.92     6.58
  LONGEST_CONTINUOUS_SEGMENT:    28       8_B - 35_B        1.90     6.59
  LCS_AVERAGE:     58.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       7_B - 23_B        0.98     6.96
  LONGEST_CONTINUOUS_SEGMENT:    17       8_B - 24_B        0.88     6.95
  LCS_AVERAGE:     29.92

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      5    8   40      3    3    5    7    7    8   10   17   21   21   23   24   29   31   33   33   38   39   41   41 
LCS_GDT     S     3_B     S     3_B      6   16   40      3    5    7    8   12   16   16   18   21   21   22   23   25   25   28   32   34   35   41   41 
LCS_GDT     Q     4_B     Q     4_B      6   17   40      3    5    7   10   15   17   19   19   21   23   26   34   35   35   37   37   38   39   41   41 
LCS_GDT     R     5_B     R     5_B      6   18   40      3    5    7   10   15   16   17   19   21   21   23   27   30   32   37   37   38   39   41   41 
LCS_GDT     L     6_B     L     6_B     11   20   40      3    5   10   14   16   18   21   28   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     F     7_B     F     7_B     17   28   40      3   10   13   16   20   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     V     8_B     V     8_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     L     9_B     L     9_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     D    10_B     D    10_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     N    11_B     N    11_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     E    12_B     E    12_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     R    13_B     R    13_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     Y    14_B     Y    14_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     D    15_B     D    15_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     S    16_B     S    16_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     F    17_B     F    17_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     I    18_B     I    18_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     T    19_B     T    19_B     17   28   40      8   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     Q    20_B     Q    20_B     17   28   40      8   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     L    21_B     L    21_B     17   28   40      8   13   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     E    22_B     E    22_B     17   28   40      9   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     A    23_B     A    23_B     17   28   40      8   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     P    24_B     P    24_B     17   28   40      8   13   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     V    25_B     V    25_B     16   28   40      5   10   12   14   18   22   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     Q    26_B     Q    26_B      4   28   40      3    3    5   10   15   22   28   31   31   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     N    27_B     N    27_B      4   28   40      3    3    4    5   10   16   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     A    28_B     A    28_B     11   28   40     10   10   18   19   23   24   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     E    29_B     E    29_B     11   28   40     10   10   16   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     G    30_B     G    30_B     11   28   40     10   10   15   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     R    31_B     R    31_B     11   28   40     10   14   18   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     E    32_B     E    32_B     11   28   40     10   10   16   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     R    33_B     R    33_B     11   28   40     10   10   16   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     L    34_B     L    34_B     11   28   40     10   10   16   23   23   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     M    35_B     M    35_B     11   28   40     10   10   11   11   18   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     A    36_B     A    36_B     11   14   40     10   10   11   11   18   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     V    37_B     V    37_B     11   14   40     10   10   11   11   18   26   28   31   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     K    38_B     K    38_B     11   14   40      3    7   11   11   12   13   15   17   32   33   33   34   35   35   37   37   38   39   41   41 
LCS_GDT     P    39_B     P    39_B      5   14   40      3    4    7   10   12   13   15   16   17   17   19   30   35   35   37   37   38   39   41   41 
LCS_GDT     E    40_B     E    40_B      5   14   40      3    4    5    8   11   11   15   16   17   17   18   18   27   30   37   37   38   39   41   41 
LCS_GDT     W    41_B     W    41_B      5   14   40      3    4    5    9   12   13   15   16   17   17   18   18   21   21   34   37   38   39   41   41 
LCS_GDT     K    42_B     K    42_B      3    4   39      3    3    3    4    4    5    5   13   13   14   15   18   18   18   20   28   33   35   41   41 
LCS_AVERAGE  LCS_A:  61.89  (  29.92   58.24   97.50 )

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     10     14     18     23     23     26     28     31     32     33     33     34     35     35     37     37     38     39     41     41 
GDT PERCENT_AT  24.39  34.15  43.90  56.10  56.10  63.41  68.29  75.61  78.05  80.49  80.49  82.93  85.37  85.37  90.24  90.24  92.68  95.12 100.00 100.00
GDT RMS_LOCAL    0.28   0.57   0.85   1.24   1.24   1.80   1.95   2.23   2.66   2.73   2.73   3.14   3.44   3.44   4.01   4.01   4.34   4.65   5.26   5.26
GDT RMS_ALL_AT  12.88   6.97   7.22   6.56   6.56   6.31   6.39   6.30   5.97   5.98   5.98   5.77   5.65   5.65   5.45   5.45   5.36   5.30   5.26   5.26

# Checking swapping
#   possible swapping detected:  D    10_B      D    10_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    15.221     0    0.470   0.492    16.844    0.000    0.000
LGA    S     3_B      S     3_B    15.004     0    0.554   0.866    18.171    0.000    0.000
LGA    Q     4_B      Q     4_B    10.695     0    0.347   0.796    12.622    0.000    6.455
LGA    R     5_B      R     5_B    10.828     0    0.108   1.549    19.684    0.714    0.260
LGA    L     6_B      L     6_B     6.520     0    0.174   1.173     8.841   17.619   16.726
LGA    F     7_B      F     7_B     3.794     0    0.054   1.346     6.317   47.262   36.797
LGA    V     8_B      V     8_B     1.636     0    0.146   0.157     2.488   75.119   71.837
LGA    L     9_B      L     9_B     0.883     0    0.053   0.841     3.469   88.214   77.857
LGA    D    10_B      D    10_B     1.238     0    0.086   1.191     4.817   81.429   67.143
LGA    N    11_B      N    11_B     1.202     0    0.068   1.392     5.928   81.429   60.417
LGA    E    12_B      E    12_B     0.926     0    0.062   0.356     1.513   88.214   87.513
LGA    R    13_B      R    13_B     0.577     0    0.026   1.278     3.727   90.476   77.489
LGA    Y    14_B      Y    14_B     0.639     0    0.029   0.164     1.827   88.214   85.238
LGA    D    15_B      D    15_B     1.280     0    0.035   0.460     1.647   79.286   78.214
LGA    S    16_B      S    16_B     0.865     0    0.038   0.591     2.471   88.214   84.683
LGA    F    17_B      F    17_B     1.181     0    0.053   0.413     2.688   79.405   70.952
LGA    I    18_B      I    18_B     2.268     0    0.023   1.089     3.168   66.786   62.024
LGA    T    19_B      T    19_B     1.803     0    0.030   0.222     2.183   77.143   72.993
LGA    Q    20_B      Q    20_B     0.496     0    0.040   1.030     6.041   92.857   67.672
LGA    L    21_B      L    21_B     2.209     0    0.061   0.795     4.059   64.881   55.893
LGA    E    22_B      E    22_B     2.260     0    0.168   0.833     7.123   62.857   43.122
LGA    A    23_B      A    23_B     0.782     0    0.052   0.073     1.301   88.333   88.762
LGA    P    24_B      P    24_B     0.170     0    0.093   0.105     2.327   86.548   80.748
LGA    V    25_B      V    25_B     3.354     0    0.139   1.065     6.217   65.238   48.707
LGA    Q    26_B      Q    26_B     4.061     0    0.096   0.910     8.517   45.119   27.249
LGA    N    27_B      N    27_B     3.737     0    0.390   1.458     8.550   43.810   25.893
LGA    A    28_B      A    28_B     3.394     0    0.663   0.623     5.527   65.119   56.381
LGA    E    29_B      E    29_B     1.868     0    0.077   0.667     3.293   72.976   66.825
LGA    G    30_B      G    30_B     2.229     0    0.107   0.107     2.247   68.810   68.810
LGA    R    31_B      R    31_B     1.992     0    0.031   1.261     9.872   72.857   41.255
LGA    E    32_B      E    32_B     1.144     0    0.079   1.149     4.470   81.548   73.175
LGA    R    33_B      R    33_B     1.066     0    0.056   1.290     6.052   86.190   63.463
LGA    L    34_B      L    34_B     0.985     0    0.035   1.102     3.820   82.024   76.131
LGA    M    35_B      M    35_B     3.141     0    0.106   0.969     5.922   50.476   46.190
LGA    A    36_B      A    36_B     3.878     0    0.175   0.175     5.915   37.976   39.048
LGA    V    37_B      V    37_B     3.899     0    0.076   1.081     5.278   36.429   41.565
LGA    K    38_B      K    38_B     7.670     4    0.227   0.272     8.889    7.500    3.651
LGA    P    39_B      P    39_B     9.975     0    0.051   0.112    10.663    0.833    1.088
LGA    E    40_B      E    40_B    12.292     0    0.487   1.326    14.942    0.000    0.000
LGA    W    41_B      W    41_B    13.617     0    0.084   0.943    15.246    0.000    0.000
LGA    K    42_B      K    42_B    15.664     0    0.092   0.603    16.724    0.000    0.000

# 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):     5.256          5.223                  5.881           55.168   48.103

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     31    2.23    64.024    64.228     1.328

LGA_LOCAL      RMSD:   2.234  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.297  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   5.256  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.902034 * X  +   0.245761 * Y  +  -0.354875 * Z  +  19.722361
  Y_new =  -0.403370 * X  +   0.187148 * Y  +  -0.895694 * Z  +  37.290119
  Z_new =  -0.153713 * X  +   0.951093 * Y  +   0.267946 * Z  +  39.318287 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.420505  0.154324  1.296189   [DEG:  -24.0931    8.8421   74.2662 ]
ZXZ: -0.377227  1.299536 -0.160231   [DEG:  -21.6135   74.4579   -9.1806 ]
 
# END of job
