
#######################################################
#                                                     #
#                        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 (  322),  selected   41 , name one
# Molecule2: number of CA atoms   81 (  640),  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      19_B - 59_B        4.58     4.58
  LCS_AVERAGE:     50.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      43_B - 59_B        1.80     6.44
  LCS_AVERAGE:     17.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      19_B - 33_B        0.42    16.21
  LONGEST_CONTINUOUS_SEGMENT:    15      45_B - 59_B        0.66     7.85
  LCS_AVERAGE:     15.51

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    19_B     A    19_B     15   16   41     12   15   15   15   15   16   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    20_B     L    20_B     15   16   41     12   15   15   17   17   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     V    21_B     V    21_B     15   16   41     12   15   15   15   15   15   18   20   24   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     H    22_B     H    22_B     15   16   41     12   15   15   15   15   15   15   15   22   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     15   16   41     12   15   15   15   15   15   17   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     F    24_B     F    24_B     15   16   41     12   15   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     M    25_B     M    25_B     15   16   41     12   15   15   15   15   15   15   20   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     T    26_B     T    26_B     15   16   41     12   15   15   15   15   15   15   15   22   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     T    27_B     T    27_B     15   16   41     12   15   15   15   15   15   17   22   24   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     15   16   41     12   15   15   15   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     S    29_B     S    29_B     15   16   41     12   15   15   15   15   15   15   22   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    30_B     L    30_B     15   16   41     12   15   15   15   15   15   15   15   21   28   32   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    31_B     L    31_B     15   16   41      9   15   15   15   15   15   15   22   24   29   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     A    32_B     A    32_B     15   16   41     12   15   15   15   15   17   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     K    33_B     K    33_B     15   16   41      6   15   15   15   15   15   17   22   24   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     E    34_B     E    34_B      7   16   41      3    5    8    8    9   11   17   22   24   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     G    35_B     G    35_B      7    8   41      4    5    8    8    9   11   17   22   23   27   33   37   40   41   41   41   41   41   41   41 
LCS_GDT     K    36_B     K    36_B      7    8   41      4    5    8    8    9   11   17   22   23   27   30   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    37_B     L    37_B      7    8   41      4    5    8    8    9   11   17   22   23   27   32   37   40   41   41   41   41   41   41   41 
LCS_GDT     V    38_B     V    38_B      7    8   41      4    5    8    8    9   11   17   22   23   26   32   37   40   41   41   41   41   41   41   41 
LCS_GDT     E    39_B     E    39_B      7    8   41      3    4    8    8    9   11   17   22   23   26   30   36   38   41   41   41   41   41   41   41 
LCS_GDT     K    40_B     K    40_B      3    4   41      3    3    4    9   11   15   17   22   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    41_B     L    41_B      3    4   41      3    6    8   11   13   15   18   22   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     I    42_B     I    42_B      3    3   41      3    3    3    3    6   11   17   22   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    43_B     L    43_B      3   17   41      3    3    3    5    7   12   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     T    44_B     T    44_B     11   17   41      3    6   12   15   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     S    45_B     S    45_B     15   17   41      5   13   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     N    46_B     N    46_B     15   17   41      5   14   16   17   18   19   21   23   25   29   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     F    47_B     F    47_B     15   17   41      5   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     T    48_B     T    48_B     15   17   41     12   14   16   17   18   19   21   23   26   29   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     E    49_B     E    49_B     15   17   41     12   14   16   17   18   19   21   23   25   29   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     R    50_B     R    50_B     15   17   41     12   14   16   17   18   19   21   23   26   29   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     T    51_B     T    51_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     V    52_B     V    52_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     R    53_B     R    53_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     R    54_B     R    54_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     A    55_B     A    55_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     F    56_B     F    56_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     D    57_B     D    57_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     L    58_B     L    58_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_GDT     V    59_B     V    59_B     15   17   41     12   14   16   17   18   19   21   23   26   30   35   37   40   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  28.02  (  15.51   17.95   50.62 )

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     15     16     17     18     19     21     23     26     30     35     37     40     41     41     41     41     41     41     41 
GDT PERCENT_AT  14.81  18.52  19.75  20.99  22.22  23.46  25.93  28.40  32.10  37.04  43.21  45.68  49.38  50.62  50.62  50.62  50.62  50.62  50.62  50.62
GDT RMS_LOCAL    0.23   0.42   0.76   0.87   1.35   1.45   2.05   2.40   3.20   3.80   3.94   4.18   4.48   4.58   4.58   4.58   4.58   4.58   4.58   4.58
GDT RMS_ALL_AT   8.61  16.21   7.95   8.12   7.01   7.13   6.36   6.06   5.11   4.63   4.80   4.69   4.59   4.58   4.58   4.58   4.58   4.58   4.58   4.58

# Checking swapping
#   possible swapping detected:  E    34_B      E    34_B
#   possible swapping detected:  F    56_B      F    56_B
#   possible swapping detected:  D    57_B      D    57_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    19_B      A    19_B     3.434     0    0.155   0.162     4.784   55.476   50.667
LGA    L    20_B      L    20_B     3.244     0    0.000   1.335     9.969   59.286   33.869
LGA    V    21_B      V    21_B     5.377     0    0.085   1.078     9.339   33.095   20.544
LGA    H    22_B      H    22_B     6.022     0    0.050   0.492    13.093   24.048   10.381
LGA    A    23_B      A    23_B     4.413     0    0.000   0.000     5.482   41.905   38.762
LGA    F    24_B      F    24_B     2.345     0    0.025   1.600    11.419   70.833   30.952
LGA    M    25_B      M    25_B     5.633     0    0.046   0.466    13.108   25.833   13.869
LGA    T    26_B      T    26_B     7.821     0    0.023   0.168    11.297   11.190    6.599
LGA    T    27_B      T    27_B     5.298     0    0.000   0.104     7.510   31.786   24.150
LGA    A    28_B      A    28_B     1.750     0    0.021   0.024     3.846   58.095   55.143
LGA    S    29_B      S    29_B     8.012     0    0.034   0.051    10.771    8.095    5.397
LGA    L    30_B      L    30_B     9.453     0    0.095   0.844    14.382    3.095    1.548
LGA    L    31_B      L    31_B     4.813     0    0.104   0.816     8.438   36.548   26.905
LGA    A    32_B      A    32_B     4.366     0    0.214   0.214     7.029   28.571   27.143
LGA    K    33_B      K    33_B    10.495     0    0.399   0.689    16.486    1.190    0.529
LGA    E    34_B      E    34_B     9.861     0    0.642   1.095    11.758    0.238    1.005
LGA    G    35_B      G    35_B    12.077     0    0.112   0.112    13.248    0.000    0.000
LGA    K    36_B      K    36_B    11.629     0    0.053   0.628    11.629    0.000    0.053
LGA    L    37_B      L    37_B    11.501     0    0.018   1.271    12.816    0.000    0.000
LGA    V    38_B      V    38_B    10.557     0    0.590   0.599    11.854    0.000    0.272
LGA    E    39_B      E    39_B    12.406     0    0.036   0.522    17.399    0.000    0.000
LGA    K    40_B      K    40_B     7.173     0    0.632   1.218     8.661    7.738   19.894
LGA    L    41_B      L    41_B     5.323     0    0.632   0.842     6.735   20.595   34.762
LGA    I    42_B      I    42_B     6.593     0    0.605   0.986    11.876   17.381    9.405
LGA    L    43_B      L    43_B     4.617     0    0.605   1.028     9.268   42.143   26.786
LGA    T    44_B      T    44_B     1.702     0    0.540   0.500     2.666   66.905   68.299
LGA    S    45_B      S    45_B     2.176     0    0.675   0.889     4.622   61.429   55.714
LGA    N    46_B      N    46_B     2.193     0    0.182   1.134     4.015   64.762   57.560
LGA    F    47_B      F    47_B     1.725     0    0.058   0.276     2.769   72.857   67.792
LGA    T    48_B      T    48_B     1.775     0    0.101   0.171     1.777   72.857   72.857
LGA    E    49_B      E    49_B     2.252     0    0.053   0.877     8.422   68.810   43.915
LGA    R    50_B      R    50_B     1.402     0    0.033   1.120     7.332   83.810   54.589
LGA    T    51_B      T    51_B     0.617     0    0.048   0.060     0.873   90.476   91.837
LGA    V    52_B      V    52_B     1.485     0    0.010   0.132     2.327   81.429   76.599
LGA    R    53_B      R    53_B     1.177     0    0.049   1.392     4.156   85.952   78.312
LGA    R    54_B      R    54_B     0.633     0    0.024   1.750     8.383   90.476   56.104
LGA    A    55_B      A    55_B     1.393     0    0.053   0.056     1.755   81.429   79.714
LGA    F    56_B      F    56_B     1.280     0    0.043   1.191     5.879   83.690   61.255
LGA    D    57_B      D    57_B     0.488     0    0.040   0.343     1.535   88.333   84.940
LGA    L    58_B      L    58_B     1.783     0    0.100   1.222     4.307   70.952   64.405
LGA    V    59_B      V    59_B     2.272     0    0.614   0.540     3.321   66.905   61.701

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     322    322  100.00                81
SUMMARY(RMSD_GDC):     4.583          4.347                  5.913           22.324   18.694

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   41   81    4.0     23    2.40    29.630    27.429     0.919

LGA_LOCAL      RMSD:   2.403  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.059  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   4.583  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.209898 * X  +  -0.571820 * Y  +  -0.793073 * Z  + 269.705750
  Y_new =   0.552812 * X  +  -0.738448 * Y  +   0.386126 * Z  + -135.800858
  Z_new =  -0.806438 * X  +  -0.357373 * Y  +   0.471108 * Z  +  60.875538 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.933674  0.938103 -0.648970   [DEG:  110.7913   53.7494  -37.1832 ]
ZXZ: -2.023888  1.080250 -1.987939   [DEG: -115.9602   61.8938 -113.9005 ]
 
# END of job
