
#######################################################
#                                                     #
#                        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   50 (  433),  selected   45 , name one
# Molecule2: number of CA atoms   76 (  680),  selected   45 , 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:    45      17_B - 66_B        4.60     4.60
  LCS_AVERAGE:     59.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      31_B - 56_B        2.00     6.23
  LONGEST_CONTINUOUS_SEGMENT:    26      32_B - 57_B        1.88     6.25
  LCS_AVERAGE:     29.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      36_B - 55_B        0.95     6.47
  LCS_AVERAGE:     22.54

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     K    17_B     K    17_B     18   20   45      9   17   17   19   21   22   27   30   31   34   37   41   42   42   42   43   44   44   44   44 
LCS_GDT     K    18_B     K    18_B     18   20   45      9   17   17   19   21   23   27   30   33   36   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     L    19_B     L    19_B     18   20   45      9   17   17   18   21   22   27   30   33   36   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    20_B     E    20_B     18   20   45      9   17   17   19   21   22   27   30   31   34   39   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    21_B     E    21_B     18   20   45      9   17   17   19   21   23   27   30   33   36   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    22_B     E    22_B     18   20   45      9   17   17   19   21   23   27   30   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     L    23_B     L    23_B     18   20   45      9   17   17   19   21   23   27   30   33   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    24_B     K    24_B     18   20   45      9   17   17   19   21   23   27   30   33   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    25_B     K    25_B     18   20   45      9   17   17   19   21   23   27   31   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     I    26_B     I    26_B     18   20   45      8   17   17   19   21   23   27   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     R    27_B     R    27_B     18   20   45      8   17   17   19   21   23   27   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    28_B     E    28_B     18   20   45      4   17   17   19   21   23   27   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     R    29_B     R    29_B     18   20   45      4   17   17   19   21   23   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     L    30_B     L    30_B     18   20   45      4   17   17   19   21   24   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     L    31_B     L    31_B     18   26   45      4   17   17   19   21   23   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     M    32_B     M    32_B     18   26   45      8   17   17   19   21   23   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     V    33_B     V    33_B     18   26   45      4   17   17   19   22   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     F    34_B     F    34_B     18   26   45      4   10   14   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     D    35_B     D    35_B      8   26   45      4    7   13   19   21   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    36_B     E    36_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    37_B     E    37_B     20   26   45      7   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     R    38_B     R    38_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     V    39_B     V    39_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    40_B     E    40_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    41_B     E    41_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     Y    42_B     Y    42_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     M    43_B     M    43_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    44_B     K    44_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     I    45_B     I    45_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     M    46_B     M    46_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    47_B     K    47_B     20   26   45      8   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    48_B     E    48_B     20   26   45      9   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     V    49_B     V    49_B     20   26   45      9   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     I    50_B     I    50_B     20   26   45      9   15   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    51_B     E    51_B     20   26   45      9   14   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    52_B     K    52_B     20   26   45      9   13   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     I    53_B     I    53_B     20   26   45      9   12   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     L    54_B     L    54_B     20   26   45      9   12   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     E    55_B     E    55_B     20   26   45      9   12   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     N    56_B     N    56_B     17   26   45      9   12   20   21   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     R    57_B     R    57_B     10   26   45      3    3    3   15   23   25   29   32   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    58_B     K    58_B      3   23   45      3    3    3    3    4    5   11   28   34   37   40   41   42   42   43   43   44   44   44   44 
LCS_GDT     K    64_B     K    64_B      3    4   45      3    4   10   13   16   20   26   26   29   30   35   35   36   39   43   43   44   44   44   44 
LCS_GDT     V    65_B     V    65_B      3    4   45      3    4   13   19   23   23   26   26   29   30   35   35   36   41   43   43   44   44   44   44 
LCS_GDT     E    66_B     E    66_B      3    4   45      0    4    4    4    8   10   10   24   27   27   28   30   31   33   36   36   37   40   40   44 
LCS_AVERAGE  LCS_A:  37.16  (  22.54   29.74   59.21 )

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      9     17     20     21     23     25     29     32     34     37     40     41     42     42     43     43     44     44     44     44 
GDT PERCENT_AT  11.84  22.37  26.32  27.63  30.26  32.89  38.16  42.11  44.74  48.68  52.63  53.95  55.26  55.26  56.58  56.58  57.89  57.89  57.89  57.89
GDT RMS_LOCAL    0.32   0.65   0.94   1.00   1.37   1.67   2.27   2.65   2.97   3.30   3.59   3.66   3.77   3.77   4.13   4.13   4.24   4.24   4.24   4.24
GDT RMS_ALL_AT   7.44   7.03   6.54   6.51   6.61   6.47   5.72   5.26   4.97   4.76   4.77   4.79   4.83   4.83   4.63   4.63   4.63   4.63   4.63   4.63

# Checking swapping
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  D    35_B      D    35_B
#   possible swapping detected:  E    37_B      E    37_B
#   possible swapping detected:  E    41_B      E    41_B
#   possible swapping detected:  E    66_B      E    66_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    17_B      K    17_B    11.897     0    0.038   0.985    15.532    0.000    0.000
LGA    K    18_B      K    18_B    10.435     0    0.016   0.855    11.063    0.476    0.423
LGA    L    19_B      L    19_B     9.609     0    0.009   0.045    10.047    1.190    1.071
LGA    E    20_B      E    20_B     9.460     0    0.033   0.774    10.200    1.548    2.381
LGA    E    21_B      E    21_B     9.141     0    0.031   0.189    11.156    3.690    1.693
LGA    E    22_B      E    22_B     7.574     0    0.052   0.146     8.236    8.810    9.206
LGA    L    23_B      L    23_B     7.061     0    0.030   0.102     7.729   11.667   10.476
LGA    K    24_B      K    24_B     7.169     0    0.024   1.024    13.533   12.619    6.455
LGA    K    25_B      K    25_B     6.182     0    0.023   0.616     7.669   22.024   16.984
LGA    I    26_B      I    26_B     4.364     0    0.069   0.090     5.258   35.952   34.524
LGA    R    27_B      R    27_B     4.508     0    0.037   1.012    10.783   34.286   20.260
LGA    E    28_B      E    28_B     4.565     0    0.081   0.809     5.801   37.381   31.905
LGA    R    29_B      R    29_B     3.362     0    0.051   1.053     5.823   51.905   42.424
LGA    L    30_B      L    30_B     2.697     0    0.068   0.132     2.829   57.143   57.143
LGA    L    31_B      L    31_B     3.475     0    0.076   1.392     4.924   46.667   48.155
LGA    M    32_B      M    32_B     3.773     0    0.057   0.601     6.493   45.000   37.381
LGA    V    33_B      V    33_B     2.617     0    0.032   1.038     4.572   57.143   54.558
LGA    F    34_B      F    34_B     3.211     0    0.126   1.212    10.387   53.571   28.745
LGA    D    35_B      D    35_B     3.345     0    0.286   1.177     6.839   49.048   33.155
LGA    E    36_B      E    36_B     2.828     0    0.458   0.516     9.818   65.476   36.667
LGA    E    37_B      E    37_B     2.975     0    0.041   0.870     4.409   55.357   48.730
LGA    R    38_B      R    38_B     2.474     0    0.013   1.079     4.427   62.857   56.407
LGA    V    39_B      V    39_B     2.696     0    0.016   0.022     3.030   57.143   56.122
LGA    E    40_B      E    40_B     2.408     0    0.040   0.965     5.930   64.762   50.582
LGA    E    41_B      E    41_B     1.872     0    0.025   1.049     4.828   70.833   57.513
LGA    Y    42_B      Y    42_B     2.034     0    0.008   1.165    10.732   68.810   36.865
LGA    M    43_B      M    43_B     1.934     0    0.029   0.725     3.571   72.857   66.310
LGA    K    44_B      K    44_B     1.664     0    0.032   1.032     6.826   75.000   56.931
LGA    I    45_B      I    45_B     1.061     0    0.035   0.079     1.221   81.429   85.952
LGA    M    46_B      M    46_B     1.409     0    0.039   0.706     1.703   79.286   77.143
LGA    K    47_B      K    47_B     1.546     0    0.034   0.041     3.626   79.286   67.249
LGA    E    48_B      E    48_B     0.628     0    0.045   0.836     2.644   85.952   80.847
LGA    V    49_B      V    49_B     1.874     0    0.017   0.092     3.141   75.000   68.503
LGA    I    50_B      I    50_B     1.869     0    0.037   0.053     2.752   72.857   66.905
LGA    E    51_B      E    51_B     0.634     0    0.068   0.058     1.191   90.476   90.529
LGA    K    52_B      K    52_B     1.834     0    0.008   1.052     9.517   70.952   46.085
LGA    I    53_B      I    53_B     2.583     0    0.066   1.273     4.830   60.952   50.833
LGA    L    54_B      L    54_B     1.588     0    0.028   0.048     3.186   77.143   69.167
LGA    E    55_B      E    55_B     1.205     0    0.066   1.291     5.108   79.405   62.434
LGA    N    56_B      N    56_B     3.293     0    0.601   0.740     5.985   50.357   41.071
LGA    R    57_B      R    57_B     1.728     0    0.069   1.648    10.190   65.000   31.602
LGA    K    58_B      K    58_B     7.469     0    0.571   1.163    15.689   10.476    4.815
LGA    K    64_B      K    64_B     8.151     0    0.626   0.750     9.636    2.619   16.402
LGA    V    65_B      V    65_B     7.280     0    0.630   0.611     8.495    7.381   13.605
LGA    E    66_B      E    66_B    11.465     0    0.635   0.915    20.022    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     396    396  100.00                76
SUMMARY(RMSD_GDC):     4.605          4.553                  5.612           27.787   23.371

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50   76    4.0     32    2.65    37.171    36.676     1.163

LGA_LOCAL      RMSD:   2.650  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.258  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:   4.605  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.845715 * X  +  -0.181199 * Y  +   0.501930 * Z  +  23.047831
  Y_new =   0.355148 * X  +   0.893147 * Y  +  -0.275968 * Z  + -20.157013
  Z_new =  -0.398292 * X  +   0.411650 * Y  +   0.819700 * Z  +  -0.635054 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.397576  0.409654  0.465403   [DEG:   22.7794   23.4714   26.6656 ]
ZXZ:  1.068096  0.609909 -0.768907   [DEG:   61.1974   34.9452  -44.0552 ]
 
# END of job
