
#######################################################
#                                                     #
#                        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   57 (  468),  selected   57 , name one
# Molecule2: number of CA atoms  260 ( 2069),  selected   57 , 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:    38      68_B - 105_B       4.83    21.15
  LCS_AVERAGE:     13.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32      68_B - 99_B        1.60    23.73
  LCS_AVERAGE:      9.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      68_B - 98_B        0.92    24.10
  LCS_AVERAGE:      8.94

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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     H    68_B     H    68_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     Y    69_B     Y    69_B     31   32   38     12   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     E    70_B     E    70_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     L    71_B     L    71_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     R    72_B     R    72_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     R    73_B     R    73_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     A    74_B     A    74_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     I    75_B     I    75_B     31   32   38     12   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     G    76_B     G    76_B     31   32   38     11   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     H    77_B     H    77_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     L    78_B     L    78_B     31   32   38     16   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     D    79_B     D    79_B     31   32   38     16   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     E    80_B     E    80_B     31   32   38      7   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     D    81_B     D    81_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     R    82_B     R    82_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     Y    83_B     Y    83_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     H    84_B     H    84_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     Q    85_B     Q    85_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     A    86_B     A    86_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     V    87_B     V    87_B     31   32   38     11   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     R    88_B     R    88_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     M    89_B     M    89_B     31   32   38     16   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     F    90_B     F    90_B     31   32   38     12   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     D    91_B     D    91_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     R    92_B     R    92_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     A    93_B     A    93_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     T    94_B     T    94_B     31   32   38     11   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     G    95_B     G    95_B     31   32   38     15   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     L    96_B     L    96_B     31   32   38     18   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     S    97_B     S    97_B     31   32   38      9   30   30   30   30   30   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     E    98_B     E    98_B     31   32   38      3    4    5    6   13   30   31   31   31   32   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     V    99_B     V    99_B     14   32   38      3    9   14   15   15   26   31   31   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     T   100_B     T   100_B     14   18   38      7   10   14   15   15   17   18   23   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     V   101_B     V   101_B     14   18   38      7   10   14   15   15   17   22   29   32   33   34   34   34   35   35   35   36   36   38   38 
LCS_GDT     Q   102_B     Q   102_B     14   18   38      7   10   14   15   15   17   18   19   20   22   27   32   34   35   35   35   36   36   38   38 
LCS_GDT     A   103_B     A   103_B     14   18   38      7   10   14   15   15   17   18   19   20   21   23   23   27   30   34   35   36   36   38   38 
LCS_GDT     V   104_B     V   104_B     14   18   38      7   10   14   15   15   17   18   19   20   21   23   23   25   26   28   30   30   34   38   38 
LCS_GDT     R   105_B     R   105_B     14   18   38      7   10   14   15   15   17   18   19   20   21   23   23   25   27   29   32   36   36   38   38 
LCS_GDT     L   106_B     L   106_B     14   18   28      7    9   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   29   31   34 
LCS_GDT     L   107_B     L   107_B     14   18   28      5    9   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     T   108_B     T   108_B     14   18   28      5   10   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     D   109_B     D   109_B     14   18   28      5   10   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     H   110_B     H   110_B     14   18   28      4   10   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     L   111_B     L   111_B     14   18   28      4   10   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     P   112_B     P   112_B     14   18   28      8   12   14   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     Q   113_B     Q   113_B     14   18   28      8   12   13   15   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     H   114_B     H   114_B     14   18   28      8   12   13   14   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     S   115_B     S   115_B     14   18   28      8   12   13   14   15   17   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     L   116_B     L   116_B     14   18   28      8   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     L   117_B     L   117_B     14   16   28      8   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     M   118_B     M   118_B     14   16   28      8   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     M   119_B     M   119_B     14   16   28      6   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     R   120_B     R   120_B     14   16   28      7   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     N   121_B     N   121_B     14   16   28      6   12   13   14   15   15   18   19   20   21   23   23   25   26   26   26   27   28   29   29 
LCS_GDT     A   122_B     A   122_B     14   16   28      8   12   13   14   15   15   18   19   20   21   22   23   25   26   26   26   27   28   29   29 
LCS_GDT     L   123_B     L   123_B     14   16   28      3   12   13   14   15   15   18   19   20   21   22   23   23   26   26   26   27   28   29   29 
LCS_GDT     P   124_B     P   124_B     14   16   28      0    3   13   14   15   15   18   19   20   21   22   23   25   26   26   26   27   28   29   29 
LCS_AVERAGE  LCS_A:  10.70  (   8.94    9.84   13.33 )

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     18     30     30     30     30     30     31     31     32     33     34     34     34     35     35     35     36     36     38     38 
GDT PERCENT_AT   6.92  11.54  11.54  11.54  11.54  11.54  11.92  11.92  12.31  12.69  13.08  13.08  13.08  13.46  13.46  13.46  13.85  13.85  14.62  14.62
GDT RMS_LOCAL    0.40   0.57   0.57   0.57   0.57   0.57   0.92   0.92   2.04   2.33   2.44   2.44   2.44   3.05   3.05   3.05   3.68   3.68   4.83   4.83
GDT RMS_ALL_AT  24.01  24.01  24.01  24.01  24.01  24.01  24.10  24.10  23.01  22.66  22.84  22.84  22.84  22.49  22.49  22.49  22.08  22.08  21.15  21.15

# Checking swapping
#   possible swapping detected:  Y    69_B      Y    69_B
#   possible swapping detected:  E    98_B      E    98_B
#   possible swapping detected:  D   109_B      D   109_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H    68_B      H    68_B     0.743     0    0.062   1.141     5.328   90.476   65.619
LGA    Y    69_B      Y    69_B     0.748     0    0.053   0.181     2.510   90.476   78.968
LGA    E    70_B      E    70_B     0.578     0    0.072   0.656     2.189   90.476   85.714
LGA    L    71_B      L    71_B     0.521     0    0.080   0.125     1.274   90.476   89.345
LGA    R    72_B      R    72_B     0.459     0    0.038   0.794     4.238  100.000   81.645
LGA    R    73_B      R    73_B     0.238     0    0.080   0.600     3.673  100.000   77.965
LGA    A    74_B      A    74_B     0.544     0    0.071   0.064     0.702   92.857   92.381
LGA    I    75_B      I    75_B     1.074     0    0.076   0.094     1.686   83.690   79.345
LGA    G    76_B      G    76_B     1.100     0    0.048   0.048     1.100   85.952   85.952
LGA    H    77_B      H    77_B     0.449     0    0.051   0.203     2.302  100.000   86.381
LGA    L    78_B      L    78_B     0.584     0    0.000   0.105     1.254   92.857   89.405
LGA    D    79_B      D    79_B     0.930     0    0.000   0.093     1.617   90.476   84.881
LGA    E    80_B      E    80_B     0.803     0    0.043   0.887     4.635   90.476   71.481
LGA    D    81_B      D    81_B     0.405     0    0.109   0.120     0.498  100.000  100.000
LGA    R    82_B      R    82_B     0.408     0    0.074   1.253     4.711   97.619   81.905
LGA    Y    83_B      Y    83_B     0.399     0    0.000   0.524     3.518  100.000   78.452
LGA    H    84_B      H    84_B     0.155     0    0.065   1.308     5.609  100.000   68.810
LGA    Q    85_B      Q    85_B     0.371     0    0.000   0.638     2.523  100.000   90.053
LGA    A    86_B      A    86_B     0.471     0    0.000   0.036     0.560  100.000   98.095
LGA    V    87_B      V    87_B     0.391     0    0.072   0.139     1.282  100.000   94.626
LGA    R    88_B      R    88_B     0.612     0    0.049   1.314     5.999   92.857   72.424
LGA    M    89_B      M    89_B     0.790     0    0.032   1.022     3.110   90.476   78.988
LGA    F    90_B      F    90_B     0.709     0    0.077   0.256     0.746   90.476   91.342
LGA    D    91_B      D    91_B     0.546     0    0.030   0.095     0.934   92.857   91.667
LGA    R    92_B      R    92_B     0.508     0    0.051   0.647     2.809   90.476   75.758
LGA    A    93_B      A    93_B     0.494     0    0.000   0.000     0.626   97.619   96.190
LGA    T    94_B      T    94_B     0.709     0    0.071   1.038     3.229   88.214   80.884
LGA    G    95_B      G    95_B     0.886     0    0.000   0.000     1.152   88.214   88.214
LGA    L    96_B      L    96_B     0.646     0    0.178   0.357     2.117   90.476   83.929
LGA    S    97_B      S    97_B     0.797     0    0.590   0.539     1.804   86.071   86.032
LGA    E    98_B      E    98_B     3.710     0    0.063   1.337    10.770   45.238   22.698
LGA    V    99_B      V    99_B     8.115     0    0.491   1.310    11.775    6.190    3.537
LGA    T   100_B      T   100_B     9.274     0    0.052   1.067    12.141    2.143    2.857
LGA    V   101_B      V   101_B    10.099     0    0.019   0.034    13.856    0.357    2.517
LGA    Q   102_B      Q   102_B    14.502     0    0.000   0.726    18.062    0.000    0.000
LGA    A   103_B      A   103_B    16.555     0    0.053   0.036    20.265    0.000    0.000
LGA    V   104_B      V   104_B    18.830     0    0.070   0.907    22.274    0.000    0.000
LGA    R   105_B      R   105_B    20.386     0    0.146   1.285    24.686    0.000    0.000
LGA    L   106_B      L   106_B    24.738     0    0.036   0.152    28.582    0.000    0.000
LGA    L   107_B      L   107_B    27.100     0    0.050   0.202    30.814    0.000    0.000
LGA    T   108_B      T   108_B    28.364     0    0.000   0.188    32.256    0.000    0.000
LGA    D   109_B      D   109_B    31.457     0    0.075   1.104    35.643    0.000    0.000
LGA    H   110_B      H   110_B    35.488     0    0.082   1.033    38.731    0.000    0.000
LGA    L   111_B      L   111_B    36.746     0    0.080   1.408    38.849    0.000    0.000
LGA    P   112_B      P   112_B    43.346     0    0.026   0.145    45.904    0.000    0.000
LGA    Q   113_B      Q   113_B    43.129     0    0.054   0.219    46.517    0.000    0.000
LGA    H   114_B      H   114_B    48.996     0    0.028   1.148    57.201    0.000    0.000
LGA    S   115_B      S   115_B    45.737     0    0.055   0.113    46.845    0.000    0.000
LGA    L   116_B      L   116_B    40.228     0    0.000   1.311    42.035    0.000    0.000
LGA    L   117_B      L   117_B    45.157     0    0.000   0.034    47.836    0.000    0.000
LGA    M   118_B      M   118_B    48.485     0    0.014   1.037    53.610    0.000    0.000
LGA    M   119_B      M   119_B    42.465     0    0.066   0.934    44.342    0.000    0.000
LGA    R   120_B      R   120_B    42.128     0    0.077   1.009    44.677    0.000    0.000
LGA    N   121_B      N   121_B    48.469     0    0.088   0.106    52.849    0.000    0.000
LGA    A   122_B      A   122_B    46.277     0    0.057   0.055    46.531    0.000    0.000
LGA    L   123_B      L   123_B    40.487     0    0.645   1.550    42.380    0.000    0.000
LGA    P   124_B      P   124_B    43.293     0    0.060   0.284    44.462    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     468    468  100.00               260
SUMMARY(RMSD_GDC):    15.093         15.026                 15.792           10.990    9.839

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  260    4.0     31    0.92    12.115    11.596     3.044

LGA_LOCAL      RMSD:   0.918  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  24.100  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  15.093  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.653971 * X  +   0.703517 * Y  +   0.278183 * Z  + -15.039845
  Y_new =  -0.275413 * X  +  -0.563880 * Y  +   0.778580 * Z  +  39.392986
  Z_new =   0.704606 * X  +   0.432554 * Y  +   0.562519 * Z  + -516.479980 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.742997 -0.781868  0.655524   [DEG: -157.1621  -44.7977   37.5588 ]
ZXZ:  2.798434  0.973367  1.020223   [DEG:  160.3384   55.7698   58.4545 ]
 
# END of job
