
#######################################################
#                                                     #
#                        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   45 (  354),  selected   45 , name one
# Molecule2: number of CA atoms  157 ( 1259),  selected   45 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    44      78_A - 121_A       4.92     5.33
  LCS_AVERAGE:     27.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      90_A - 110_A       1.77    10.30
  LCS_AVERAGE:      9.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      96_A - 110_A       0.94     9.58
  LCS_AVERAGE:      6.85

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     E    78_A     E    78_A     11   11   44      8   10   11   11   16   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A    79_A     A    79_A     11   11   44      8   10   11   11   14   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     F    80_A     F    80_A     11   11   44      8   10   11   11   14   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     N    81_A     N    81_A     11   11   44      8   10   11   11   16   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A    82_A     A    82_A     11   11   44      8   10   11   11   16   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     Y    83_A     Y    83_A     11   11   44      8   10   11   11   14   18   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     L    84_A     L    84_A     11   11   44      8   10   11   11   14   19   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     E    85_A     E    85_A     11   11   44      8   10   11   11   14   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A    86_A     A    86_A     11   11   44      4   10   11   11   14   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     L    87_A     L    87_A     11   11   44      7   10   11   11   12   14   20   29   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     G    88_A     G    88_A     11   11   44      3    9   11   12   16   19   25   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     P    89_A     P    89_A      4   10   44      3    4   11   15   16   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     D    90_A     D    90_A      7   21   44      4    8   12   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A    91_A     A    91_A      7   21   44      4    4    9   13   19   21   21   26   27   28   29   32   36   38   39   41   42   43   43   43 
LCS_GDT     V    92_A     V    92_A      7   21   44      4    6   13   17   19   21   24   26   27   29   31   37   38   38   40   41   42   43   43   43 
LCS_GDT     R    93_A     R    93_A      7   21   44      4    9   13   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     T    94_A     T    94_A      7   21   44      4    6    9   11   17   21   24   28   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     V    95_A     V    95_A      7   21   44      4    6    9   11   16   21   24   26   27   29   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     Q    96_A     Q    96_A     15   21   44      4   10   14   16   19   21   24   26   28   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     D    97_A     D    97_A     15   21   44      4   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     L    98_A     L    98_A     15   21   44      4   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     T    99_A     T    99_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     R   100_A     R   100_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     R   101_A     R   101_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     F   102_A     F   102_A     15   21   44      4   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     V   103_A     V   103_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     D   104_A     D   104_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     V   105_A     V   105_A     15   21   44      6   12   14   17   19   21   25   30   32   33   34   37   38   38   40   41   42   43   43   43 
LCS_GDT     I   106_A     I   106_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     R   107_A     R   107_A     15   21   44      6   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A   108_A     A   108_A     15   21   44      4   11   14   17   19   21   24   27   30   32   34   37   38   38   40   41   42   43   43   43 
LCS_GDT     D   109_A     D   109_A     15   21   44      5   10   14   17   19   21   23   26   27   29   33   37   38   38   40   41   41   43   43   43 
LCS_GDT     P   110_A     P   110_A     15   21   44      8   12   14   17   19   21   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     E   111_A     E   111_A     10   20   44      8    9   10   13   16   20   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A   112_A     A   112_A     10   17   44      8    9   10   15   16   19   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     I   113_A     I   113_A     10   17   44      8    9   10   10   13   18   25   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     A   114_A     A   114_A     10   12   44      8    9   10   10   14   18   25   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     K   115_A     K   115_A     10   12   44      8    9   10   10   13   19   26   30   32   33   35   37   38   38   40   41   42   43   43   43 
LCS_GDT     L   116_A     L   116_A     10   12   44      8    9   10   10   11   12   16   22   28   33   35   36   38   38   40   41   42   43   43   43 
LCS_GDT     L   117_A     L   117_A     10   12   44      8    9   10   10   11   12   13   16   20   24   29   35   38   38   40   41   42   43   43   43 
LCS_GDT     N   118_A     N   118_A     10   12   44      4    9   10   10   11   12   13   18   24   26   35   36   38   38   40   41   42   43   43   43 
LCS_GDT     I   119_A     I   119_A      3    5   44      3    3    3    4    5    6    7    9   12   14   16   21   25   30   39   40   42   43   43   43 
LCS_GDT     S   120_A     S   120_A      3    5   44      3    3    3    4    4    5    6    8    9   10   12   14   17   18   23   26   42   43   43   43 
LCS_GDT     K   121_A     K   121_A      3    3   44      3    3    3    3    4    4    6    6    8    9   10   11   11   14   14   16   17   21   39   42 
LCS_GDT     E   122_A     E   122_A      3    3   12      3    3    3    3    3    4    4    6    8    8   10   11   11   11   11   12   15   15   15   15 
LCS_AVERAGE  LCS_A:  14.79  (   6.85    9.94   27.57 )

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      8     12     14     17     19     21     26     30     32     33     35     37     38     38     40     41     42     43     43     43 
GDT PERCENT_AT   5.10   7.64   8.92  10.83  12.10  13.38  16.56  19.11  20.38  21.02  22.29  23.57  24.20  24.20  25.48  26.11  26.75  27.39  27.39  27.39
GDT RMS_LOCAL    0.30   0.71   0.84   1.31   1.58   1.77   2.70   2.92   3.07   3.20   3.55   3.63   3.74   3.74   4.05   4.20   4.55   4.65   4.65   4.65
GDT RMS_ALL_AT  15.18   8.52   9.21   9.24   9.93  10.30   5.56   5.53   5.46   5.50   5.54   5.46   5.47   5.47   5.54   5.50   5.42   5.40   5.40   5.40

# Checking swapping
#   possible swapping detected:  F    80_A      F    80_A
#   possible swapping detected:  Y    83_A      Y    83_A
#   possible swapping detected:  D    90_A      D    90_A
#   possible swapping detected:  D    97_A      D    97_A
#   possible swapping detected:  D   109_A      D   109_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    78_A      E    78_A     3.295     0    0.056   0.918     9.184   55.357   32.275
LGA    A    79_A      A    79_A     3.443     0    0.062   0.069     4.254   53.571   50.286
LGA    F    80_A      F    80_A     2.308     0    0.036   1.275     5.343   62.857   51.212
LGA    N    81_A      N    81_A     1.816     0    0.056   0.069     4.048   72.857   59.881
LGA    A    82_A      A    82_A     2.400     0    0.018   0.018     3.552   66.786   62.095
LGA    Y    83_A      Y    83_A     3.339     0    0.025   0.342     5.705   50.119   36.905
LGA    L    84_A      L    84_A     3.360     0    0.041   1.352     6.481   50.119   46.190
LGA    E    85_A      E    85_A     2.436     0    0.038   0.477     3.724   59.167   57.407
LGA    A    86_A      A    86_A     2.990     0    0.198   0.204     3.902   52.143   51.714
LGA    L    87_A      L    87_A     5.268     0    0.206   0.388     6.698   25.714   23.036
LGA    G    88_A      G    88_A     4.268     0    0.657   0.657     5.017   37.619   37.619
LGA    P    89_A      P    89_A     2.624     0    0.111   0.128     4.678   56.786   57.415
LGA    D    90_A      D    90_A     3.382     0    0.623   0.773     5.074   43.095   43.393
LGA    A    91_A      A    91_A     8.715     0    0.060   0.058    11.076    5.595    4.476
LGA    V    92_A      V    92_A     7.358     0    0.280   1.236    10.150   16.905   10.476
LGA    R    93_A      R    93_A     1.037     0    0.071   1.419     5.829   80.000   58.658
LGA    T    94_A      T    94_A     4.793     0    0.016   0.042     8.782   36.071   23.469
LGA    V    95_A      V    95_A     6.859     0    0.041   0.035    10.785   19.405   11.293
LGA    Q    96_A      Q    96_A     5.477     0    0.023   0.995     9.768   30.238   16.402
LGA    D    97_A      D    97_A     2.959     0    0.079   1.036     5.558   53.690   45.833
LGA    L    98_A      L    98_A     2.471     0    0.066   0.772     6.018   68.810   48.512
LGA    T    99_A      T    99_A     2.556     0    0.040   0.162     4.106   62.857   55.510
LGA    R   100_A      R   100_A     2.547     0    0.034   0.912     8.793   62.857   36.061
LGA    R   101_A      R   101_A     2.370     0    0.051   1.304     4.174   66.786   55.022
LGA    F   102_A      F   102_A     1.661     0    0.056   0.260     2.937   72.857   66.364
LGA    V   103_A      V   103_A     2.007     0    0.024   0.228     3.407   70.833   63.946
LGA    D   104_A      D   104_A     3.077     0    0.039   0.125     4.735   52.024   43.929
LGA    V   105_A      V   105_A     3.660     0    0.060   0.071     5.043   46.667   41.905
LGA    I   106_A      I   106_A     2.698     0    0.181   0.627     3.062   59.048   58.274
LGA    R   107_A      R   107_A     2.857     0    0.039   1.250    10.841   50.595   30.390
LGA    A   108_A      A   108_A     5.702     0    0.099   0.116     6.980   22.262   21.238
LGA    D   109_A      D   109_A     6.629     0    0.542   1.337    11.095   24.524   12.976
LGA    P   110_A      P   110_A     2.752     0    0.047   0.321     5.787   62.143   50.476
LGA    E   111_A      E   111_A     2.689     0    0.028   1.100     5.661   67.143   50.847
LGA    A   112_A      A   112_A     2.835     0    0.031   0.036     4.289   55.357   51.714
LGA    I   113_A      I   113_A     4.134     0    0.030   0.101     6.342   40.476   31.667
LGA    A   114_A      A   114_A     3.712     0    0.018   0.025     5.320   39.167   41.333
LGA    K   115_A      K   115_A     3.374     0    0.024   0.214     5.309   40.833   47.143
LGA    L   116_A      L   116_A     6.202     0    0.035   1.374     8.389   15.833   13.869
LGA    L   117_A      L   117_A     8.593     0    0.019   0.092    10.490    4.048    2.738
LGA    N   118_A      N   118_A     8.110     0    0.344   0.780    11.547    5.952    3.571
LGA    I   119_A      I   119_A     9.825     0    0.612   1.413    15.137    0.595    0.298
LGA    S   120_A      S   120_A    11.221     0    0.668   0.912    14.151    0.000    0.000
LGA    K   121_A      K   121_A    12.243     0    0.354   0.813    14.143    0.000    0.000
LGA    E   122_A      E   122_A    15.358     0    0.596   0.867    18.736    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     354    354  100.00               157
SUMMARY(RMSD_GDC):     5.299          5.318                  6.092           12.228   10.241

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45  157    4.0     30    2.92    15.924    14.801     0.994

LGA_LOCAL      RMSD:   2.919  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.530  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:   5.299  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.000965 * X  +  -0.782881 * Y  +  -0.622171 * Z  +  38.243393
  Y_new =  -0.866488 * X  +  -0.309931 * Y  +   0.391332 * Z  +   0.329182
  Z_new =  -0.499196 * X  +   0.539482 * Y  +  -0.678058 * Z  + -17.070200 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.571910  0.522671  2.469523   [DEG:  -90.0638   29.9468  141.4933 ]
ZXZ: -2.132251  2.315913 -0.746632   [DEG: -122.1690  132.6921  -42.7789 ]
 
# END of job
