
#######################################################
#                                                     #
#                        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   56 (  447),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        3.81     3.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       5_B - 41_B        1.94     4.60
  LCS_AVERAGE:     80.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26       5_B - 30_B        0.97     5.54
  LONGEST_CONTINUOUS_SEGMENT:    26       6_B - 31_B        0.98     5.37
  LONGEST_CONTINUOUS_SEGMENT:    26       7_B - 32_B        0.97     5.13
  LCS_AVERAGE:     45.97

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   41   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     26   37   43     13   18   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     26   37   43     13   19   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     26   37   43     13   19   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     26   37   43     13   19   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     26   37   43     13   19   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     26   37   43     13   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     26   37   43     13   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     26   37   43     14   20   26   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     26   37   43     14   20   25   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     26   37   43     12   20   25   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     22   37   43      4    7   18   28   31   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      6   37   43      4    5    6   13   28   32   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      8   37   43      5   18   22   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      8   37   43      5   20   22   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      8   37   43      5   20   24   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      8   37   43      5   20   22   29   32   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      8   37   43      5   18   22   25   31   34   35   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      8   37   43      4   10   21   24   27   30   33   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      8   37   43      4    8   17   24   28   32   33   37   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      8   34   43      4    7   13   21   25   27   31   35   36   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      8   31   43      4    7   11   17   24   26   29   33   36   37   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   29   43      4    7   11   17   22   25   29   33   34   37   38   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   13   43      3    6    8   14   17   20   27   29   31   34   35   37   38   39   41   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   12   43      3    3    4    5    5    5    8   18   23   28   30   36   37   39   40   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5    5   32   33   36   36   39   40   42   43   43   43   43 
LCS_AVERAGE  LCS_A:  75.54  (  45.97   80.64  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     14     20     26     29     32     34     35     37     37     38     39     40     40     40     41     42     43     43     43     43 
GDT PERCENT_AT  32.56  46.51  60.47  67.44  74.42  79.07  81.40  86.05  86.05  88.37  90.70  93.02  93.02  93.02  95.35  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.25   0.53   0.97   1.10   1.33   1.53   1.65   1.94   1.94   2.19   2.49   2.75   2.75   2.75   3.15   3.74   3.81   3.81   3.81   3.81
GDT RMS_ALL_AT   4.66   4.62   5.54   5.19   4.89   4.79   4.80   4.60   4.60   4.43   4.24   4.08   4.08   4.08   3.92   3.82   3.81   3.81   3.81   3.81

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.563     0    0.033   0.181     3.527   59.048   54.921
LGA    L     6_B      L     6_B     3.008     0    0.034   0.868     3.609   57.262   55.476
LGA    E     7_B      E     7_B     2.556     0    0.032   1.106     7.330   65.000   48.307
LGA    T     8_B      T     8_B     0.993     0    0.062   1.230     2.876   86.071   78.435
LGA    K     9_B      K     9_B     1.285     0    0.010   0.133     2.740   81.429   73.122
LGA    K    10_B      K    10_B     1.651     0    0.015   0.944     5.807   77.143   60.582
LGA    A    11_B      A    11_B     1.501     0    0.017   0.017     1.696   79.286   78.000
LGA    Y    12_B      Y    12_B     0.716     0    0.038   0.081     2.770   90.476   78.968
LGA    A    13_B      A    13_B     0.610     0    0.006   0.014     1.012   90.476   88.667
LGA    A    14_B      A    14_B     1.366     0    0.032   0.035     1.933   81.548   79.810
LGA    R    15_B      R    15_B     1.846     0    0.022   1.205     5.198   72.976   65.108
LGA    T    16_B      T    16_B     1.748     0    0.069   0.081     1.945   72.857   74.082
LGA    R    17_B      R    17_B     1.098     0    0.040   0.740     4.104   81.429   63.550
LGA    R    18_B      R    18_B     1.439     0    0.023   1.279     6.651   77.143   58.788
LGA    S    19_B      S    19_B     2.119     0    0.039   0.702     2.546   70.833   70.317
LGA    N    20_B      N    20_B     1.858     0    0.043   0.359     2.043   77.143   75.060
LGA    Y    21_B      Y    21_B     0.691     0    0.082   0.221     4.037   88.214   72.659
LGA    A    22_B      A    22_B     1.028     0    0.008   0.014     1.405   85.952   85.048
LGA    A    23_B      A    23_B     1.342     0    0.024   0.025     1.679   81.429   79.714
LGA    S    24_B      S    24_B     1.305     0    0.064   0.724     1.385   81.429   82.937
LGA    L    25_B      L    25_B     0.805     0    0.036   0.065     0.951   90.476   90.476
LGA    R    26_B      R    26_B     0.765     0    0.045   1.021     5.031   90.476   68.485
LGA    L    27_B      L    27_B     1.056     0    0.024   0.205     1.760   83.690   81.488
LGA    E    28_B      E    28_B     0.901     0    0.029   1.102     4.662   88.214   78.095
LGA    G    29_B      G    29_B     0.815     0    0.080   0.080     0.820   90.476   90.476
LGA    F    30_B      F    30_B     0.718     0    0.038   0.060     1.146   92.857   88.874
LGA    K    31_B      K    31_B     0.715     0    0.061   0.619     3.843   90.476   76.085
LGA    V    32_B      V    32_B     0.391     0    0.018   0.224     2.098   88.571   84.422
LGA    T    33_B      T    33_B     2.514     0    0.053   1.119     5.473   65.000   54.218
LGA    F    34_B      F    34_B     3.854     0    0.614   0.436     6.720   45.238   28.268
LGA    A    35_B      A    35_B     1.700     0    0.183   0.193     3.025   75.000   70.000
LGA    D    36_B      D    36_B     1.380     0    0.038   0.186     2.019   79.286   77.202
LGA    G    37_B      G    37_B     1.378     0    0.097   0.097     2.034   75.119   75.119
LGA    E    38_B      E    38_B     1.733     0    0.036   0.866     3.369   66.905   67.831
LGA    R    39_B      R    39_B     2.871     0    0.118   1.373     4.848   55.476   50.346
LGA    K    40_B      K    40_B     4.399     0    0.068   0.842    12.746   37.262   20.582
LGA    M    41_B      M    41_B     4.572     0    0.034   1.271     5.727   29.048   41.012
LGA    P    42_B      P    42_B     6.814     0    0.045   0.339     7.272   13.452   14.082
LGA    T    43_B      T    43_B     8.560     0    0.076   1.100    11.081    3.214    2.245
LGA    R    44_B      R    44_B     9.288     0    0.602   0.928     9.815    2.024    2.035
LGA    E    45_B      E    45_B    12.825     0    0.448   1.131    17.598    0.000    0.000
LGA    E    46_B      E    46_B    14.181     0    0.596   1.435    16.644    0.000    0.000
LGA    V    47_B      V    47_B    14.149     0    0.517   1.416    16.153    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     3.808          3.724                  4.432           65.568   60.114

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     37    1.94    74.419    78.605     1.812

LGA_LOCAL      RMSD:   1.942  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.604  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.808  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.855041 * X  +   0.244531 * Y  +   0.457285 * Z  +  19.340302
  Y_new =   0.267625 * X  +   0.963410 * Y  +  -0.014767 * Z  + -59.497349
  Z_new =  -0.444163 * X  +   0.109754 * Y  +  -0.889198 * Z  +  16.018236 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.838255  0.460240  3.018783   [DEG:  162.6200   26.3698  172.9635 ]
ZXZ:  1.538514  2.666385 -1.328546   [DEG:   88.1504  152.7726  -76.1201 ]
 
# END of job
