
#######################################################
#                                                     #
#                        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   36 (  302),  selected   36 , name one
# Molecule2: number of CA atoms   87 (  706),  selected   36 , 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:    21      30_A - 50_A        4.90     8.98
  LONGEST_CONTINUOUS_SEGMENT:    21      41_A - 61_A        4.77    13.74
  LCS_AVERAGE:     23.79

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      45_A - 51_A        1.96    18.66
  LONGEST_CONTINUOUS_SEGMENT:     7      53_A - 59_A        1.78    14.42
  LCS_AVERAGE:      6.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5      46_A - 50_A        0.39    20.41
  LONGEST_CONTINUOUS_SEGMENT:     5      54_A - 58_A        0.58    19.06
  LONGEST_CONTINUOUS_SEGMENT:     5      55_A - 59_A        0.74    15.57
  LCS_AVERAGE:      4.63

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   36
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     I    26_A     I    26_A      4    6   17      3    4    4    5    9   12   13   14   16   17   19   19   20   22   23   24   25   27   28   30 
LCS_GDT     R    27_A     R    27_A      4    6   18      3    4    4    5    8   10   10   13   16   16   17   19   20   22   24   27   29   30   32   33 
LCS_GDT     R    28_A     R    28_A      4    6   19      3    4    4    5    6    7    8   10   11   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     I    29_A     I    29_A      4    6   19      3    4    4    5    6    7    9   10   11   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     P    30_A     P    30_A      4    6   21      3    4    4    5    5    7    9   10   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     I    31_A     I    31_A      4    6   21      3    4    4    5    6    7    9   10   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     H    32_A     H    32_A      4    4   21      3    3    4    4    5    6    8   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     N    33_A     N    33_A      4    5   21      4    4    4    4    4    6    8   11   12   13   15   17   19   23   24   26   27   27   30   31 
LCS_GDT     E    34_A     E    34_A      4    5   21      4    4    4    4    5    6    8   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     D    35_A     D    35_A      4    5   21      4    4    4    4    4    6    8   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     I    36_A     I    36_A      4    5   21      4    4    4    4    5    6    8   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     T    37_A     T    37_A      3    5   21      3    3    3    4    4    7    8   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     Y    38_A     Y    38_A      3    4   21      3    4    4    5    6    7    9   10   11   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     D    39_A     D    39_A      4    4   21      3    4    4    5    6    7    9   11   12   14   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     E    40_A     E    40_A      4    4   21      3    3    4    4    4    5    6    9   12   13   17   20   21   23   25   27   29   30   32   33 
LCS_GDT     L    41_A     L    41_A      4    4   21      3    3    4    4    4    5    6   11   12   13   17   19   21   23   25   27   29   30   32   33 
LCS_GDT     V    42_A     V    42_A      4    4   21      1    3    5    6    8   10   11   13   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     L    43_A     L    43_A      3    3   21      1    3    5    6    8   10   11   13   16   16   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     M    44_A     M    44_A      3    4   21      3    3    4    4    6    9   11   14   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     M    45_A     M    45_A      3    7   21      3    3    3    5    9   12   13   15   16   17   19   19   20   22   24   26   27   29   32   33 
LCS_GDT     Q    46_A     Q    46_A      5    7   21      4    5    5    5    8   12   13   15   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     R    47_A     R    47_A      5    7   21      4    5    5    5    9   12   13   15   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     V    48_A     V    48_A      5    7   21      4    5    5    5    7   10   13   15   16   17   19   19   20   23   24   26   29   30   32   33 
LCS_GDT     F    49_A     F    49_A      5    7   21      4    5    5    5    7    9   13   15   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     R    50_A     R    50_A      5    7   21      4    5    5    6    9   12   13   15   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     G    51_A     G    51_A      3    7   21      3    3    5    6    9   12   13   15   16   17   19   19   21   23   25   27   29   30   32   33 
LCS_GDT     K    52_A     K    52_A      3    5   21      3    3    5    6    9   12   13   15   16   17   19   19   20   22   25   27   29   30   32   33 
LCS_GDT     L    53_A     L    53_A      3    7   21      3    3    3    5    8   12   13   15   16   17   19   19   20   22   23   24   29   30   32   33 
LCS_GDT     L    54_A     L    54_A      5    7   21      4    5    5    6    7    8   12   15   16   17   19   19   20   21   23   24   26   29   30   33 
LCS_GDT     S    55_A     S    55_A      5    7   21      4    5    5    6    8   11   13   15   16   17   19   19   20   22   25   27   29   30   32   33 
LCS_GDT     N    56_A     N    56_A      5    7   21      4    5    5    6    8   12   13   15   16   17   19   19   20   22   23   27   29   30   32   33 
LCS_GDT     D    57_A     D    57_A      5    7   21      4    5    5    6    9   12   13   15   16   17   19   19   20   22   25   27   29   30   32   33 
LCS_GDT     E    58_A     E    58_A      5    7   21      3    5    5    6    9   12   13   15   16   17   19   20   21   23   25   27   29   30   32   33 
LCS_GDT     V    59_A     V    59_A      5    7   21      3    5    5    6    9   12   13   15   16   17   19   19   21   23   25   27   29   30   32   33 
LCS_GDT     T    60_A     T    60_A      3    4   21      3    3    3    5    6    7    8    8   16   17   17   18   20   23   24   26   27   29   32   33 
LCS_GDT     I    61_A     I    61_A      3    4   21      3    3    3    3    4    5    7    8   16   17   17   18   19   21   22   24   26   26   27   29 
LCS_AVERAGE  LCS_A:  11.63  (   4.63    6.48   23.79 )

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      4      5      5      6      9     12     13     15     16     17     19     20     21     23     25     27     29     30     32     33 
GDT PERCENT_AT   4.60   5.75   5.75   6.90  10.34  13.79  14.94  17.24  18.39  19.54  21.84  22.99  24.14  26.44  28.74  31.03  33.33  34.48  36.78  37.93
GDT RMS_LOCAL    0.12   0.39   0.39   1.04   1.97   2.26   2.36   2.88   3.01   3.15   3.73   4.76   4.91   5.13   5.60   5.87   6.14   6.29   6.60   6.72
GDT RMS_ALL_AT  19.75  20.41  20.41  17.08  14.60  14.86  14.88  16.70  15.75  15.83  13.57   7.80   7.69   7.72   7.57   7.48   7.56   7.54   7.47   7.48

# Checking swapping
#   possible swapping detected:  D    35_A      D    35_A
#   possible swapping detected:  Y    38_A      Y    38_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  F    49_A      F    49_A
#   possible swapping detected:  E    58_A      E    58_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    26_A      I    26_A     5.831     0    0.151   1.339     9.330   16.190   14.464
LGA    R    27_A      R    27_A    12.086     0    0.160   1.510    14.516    0.119    0.043
LGA    R    28_A      R    28_A    18.265     0    0.073   1.544    26.333    0.000    0.000
LGA    I    29_A      I    29_A    23.588     0    0.122   1.085    25.218    0.000    0.000
LGA    P    30_A      P    30_A    29.327     0    0.637   0.795    31.598    0.000    0.000
LGA    I    31_A      I    31_A    30.725     0    0.608   0.759    31.180    0.000    0.000
LGA    H    32_A      H    32_A    30.734     0    0.070   0.892    31.298    0.000    0.000
LGA    N    33_A      N    33_A    32.022     0    0.594   1.207    32.850    0.000    0.000
LGA    E    34_A      E    34_A    33.240     0    0.162   0.979    40.184    0.000    0.000
LGA    D    35_A      D    35_A    30.619     0    0.262   0.871    31.721    0.000    0.000
LGA    I    36_A      I    36_A    25.018     0    0.581   1.051    27.237    0.000    0.000
LGA    T    37_A      T    37_A    25.529     0    0.599   1.023    29.833    0.000    0.000
LGA    Y    38_A      Y    38_A    22.264     0    0.026   1.499    23.636    0.000    0.000
LGA    D    39_A      D    39_A    18.966     0    0.610   0.604    20.484    0.000    0.000
LGA    E    40_A      E    40_A    19.585     0    0.049   1.221    23.323    0.000    0.000
LGA    L    41_A      L    41_A    13.749     0    0.614   0.612    15.910    0.000    0.179
LGA    V    42_A      V    42_A     9.490     0    0.603   0.619    10.562    2.857    1.905
LGA    L    43_A      L    43_A    10.504     0    0.621   0.780    15.412    0.119    0.060
LGA    M    44_A      M    44_A     7.742     0    0.649   1.206    12.271   16.071    8.690
LGA    M    45_A      M    45_A     2.241     0    0.087   0.408     4.895   55.714   51.786
LGA    Q    46_A      Q    46_A     2.599     0    0.623   0.980    10.382   61.071   34.603
LGA    R    47_A      R    47_A     2.166     0    0.092   1.126     7.030   75.238   43.853
LGA    V    48_A      V    48_A     3.681     0    0.132   1.150     7.118   48.452   38.095
LGA    F    49_A      F    49_A     3.721     0    0.417   1.478     5.264   44.167   43.160
LGA    R    50_A      R    50_A     2.532     0    0.539   0.955    13.541   65.000   28.355
LGA    G    51_A      G    51_A     2.088     0    0.622   0.622     2.088   75.238   75.238
LGA    K    52_A      K    52_A     3.005     0    0.650   0.926     6.991   50.357   40.265
LGA    L    53_A      L    53_A     3.185     0    0.626   1.530     9.436   50.357   30.952
LGA    L    54_A      L    54_A     4.164     0    0.665   0.960     9.999   54.167   31.429
LGA    S    55_A      S    55_A     2.923     0    0.071   0.664     6.212   63.333   52.302
LGA    N    56_A      N    56_A     1.930     0    0.220   0.985     2.790   72.976   74.345
LGA    D    57_A      D    57_A     0.948     0    0.059   0.832     4.983   95.238   70.714
LGA    E    58_A      E    58_A     2.563     0    0.612   0.811     5.927   54.048   40.212
LGA    V    59_A      V    59_A     3.624     0    0.617   0.585     7.388   55.833   38.844
LGA    T    60_A      T    60_A     5.090     0    0.024   0.184     8.886   25.238   17.279
LGA    I    61_A      I    61_A     6.230     0    0.032   0.637     7.881   14.405   21.131

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       36     144    144  100.00     302    302  100.00                87
SUMMARY(RMSD_GDC):     7.448          7.237                  8.738           11.450    8.712

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   36   87    4.0     15    2.88    15.230    13.200     0.504

LGA_LOCAL      RMSD:   2.875  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.701  Number of assigned atoms:   36 
Std_ASGN_ATOMS RMSD:   7.448  Standard rmsd on all 36 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.519693 * X  +  -0.853104 * Y  +  -0.046188 * Z  + -19.028004
  Y_new =   0.772817 * X  +   0.492457 * Y  +  -0.400300 * Z  +  49.198685
  Z_new =   0.364243 * X  +   0.172339 * Y  +   0.915219 * Z  + -28.717365 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.978790 -0.372820  0.186124   [DEG:   56.0805  -21.3610   10.6641 ]
ZXZ: -0.114875  0.414744  1.128865   [DEG:   -6.5818   23.7631   64.6792 ]
 
# END of job
