
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , 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:    29      30_A - 58_A        4.52    14.97
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.46    15.21
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.54    15.20
  LCS_AVERAGE:     29.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     1_A     A     1_A      3   14   17      3    3    3    5   11   25   31   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     25   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   26   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    3   15   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      3   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    8   10   16   27   31   36   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     12   14   14   14   15   15   17   25   30   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   24   28   33   40   42   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   26   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   25   27   31   34   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     13   14   14   14   15   15   17   19   20   22   22   22   22   23   24   27   31   33   37   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    5   11   14   15   15   17   19   20   22   22   22   26   29   38   41   43   44   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   16   19   20   22   22   26   28   33   41   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   14   17   19   20   22   22   22   22   34   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    9   12   27   31   37   40   40   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6    9   17   36   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      3   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     24   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     30   32   34   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    5   16   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.38  (  29.49   32.82   43.85 )

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     30     32     34     36     37     37     37     37     39     39     41     41     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  51.72  55.17  58.62  62.07  63.79  63.79  63.79  63.79  67.24  67.24  70.69  70.69  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.27   0.31   0.47   0.64   0.76   0.76   0.76   0.76   1.69   1.69   2.33   2.33   2.74   2.74   3.23   3.66   3.66   4.01   4.42   4.42
GDT RMS_ALL_AT  15.23  15.23  15.20  15.20  15.21  15.21  15.21  15.21  15.12  15.12  14.93  14.93  14.90  14.90  14.85  14.76  14.76  14.64  14.53  14.53

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.854     0    0.506   0.551     8.350   21.667   18.762
LGA    E     2_A      E     2_A     0.213     0    0.652   1.157     7.003   89.286   54.127
LGA    Y     3_A      Y     3_A     0.149     0    0.016   0.126     0.925  100.000   96.825
LGA    V     4_A      V     4_A     0.133     0    0.029   0.037     0.311  100.000  100.000
LGA    R     5_A      R     5_A     0.087     0    0.023   0.190     1.861  100.000   93.290
LGA    A     6_A      A     6_A     0.350     0    0.055   0.057     0.454  100.000  100.000
LGA    L     7_A      L     7_A     0.348     0    0.040   0.069     0.492  100.000  100.000
LGA    F     8_A      F     8_A     0.521     0    0.030   0.104     0.627   92.857   92.208
LGA    D     9_A      D     9_A     0.523     0    0.067   0.362     2.075   90.476   87.321
LGA    H    10_A      H    10_A     0.638     0    0.021   1.141     2.477   90.476   85.286
LGA    T    11_A      T    11_A     1.104     0    0.643   0.974     3.152   75.833   73.537
LGA    G    12_A      G    12_A     1.510     0    0.075   0.075     1.596   77.143   77.143
LGA    H    13_A      H    13_A     2.503     0    0.630   1.486     4.322   55.952   53.905
LGA    D    14_A      D    14_A     1.684     0    0.090   1.225     5.352   55.952   53.929
LGA    E    15_A      E    15_A     7.387     0    0.712   0.663    14.205   14.643    6.825
LGA    Q    16_A      Q    16_A     8.258     0    0.655   1.206    10.218    3.333    2.963
LGA    E    17_A      E    17_A    12.052     0    0.046   1.002    15.796    0.000    0.000
LGA    L    18_A      L    18_A    19.168     0    0.095   1.353    23.339    0.000    0.000
LGA    P    19_A      P    19_A    24.775     0    0.045   0.085    27.533    0.000    0.000
LGA    F    20_A      F    20_A    30.644     0    0.036   1.450    32.796    0.000    0.000
LGA    K    21_A      K    21_A    37.507     0    0.031   0.131    40.038    0.000    0.000
LGA    K    22_A      K    22_A    40.317     0    0.026   0.520    48.584    0.000    0.000
LGA    G    23_A      G    23_A    42.274     0    0.017   0.017    42.276    0.000    0.000
LGA    E    24_A      E    24_A    38.759     0    0.018   1.027    39.585    0.000    0.000
LGA    I    25_A      I    25_A    36.421     0    0.085   0.644    41.257    0.000    0.000
LGA    L    26_A      L    26_A    29.986     0    0.024   0.082    32.048    0.000    0.000
LGA    R    27_A      R    27_A    28.378     0    0.084   0.549    32.600    0.000    0.000
LGA    I    28_A      I    28_A    21.300     0    0.008   0.067    24.017    0.000    0.000
LGA    R    29_A      R    29_A    21.204     0    0.604   1.130    30.556    0.000    0.000
LGA    D    30_A      D    30_A    17.234     0    0.684   0.964    21.797    0.000    0.000
LGA    K    31_A      K    31_A    15.097     0    0.270   0.275    22.141    0.000    0.000
LGA    P    32_A      P    32_A    13.999     0    0.070   0.366    16.184    0.000    0.000
LGA    E    33_A      E    33_A    11.222     0    0.689   1.047    13.795    0.119    0.053
LGA    E    34_A      E    34_A     7.629     0    0.221   1.102    10.629   13.810    7.037
LGA    Q    35_A      Q    35_A     1.111     0    0.647   0.667     5.291   82.857   67.513
LGA    L    36_A      L    36_A     0.673     0    0.176   1.122     2.647   90.595   79.821
LGA    W    37_A      W    37_A     0.462     0    0.061   0.266     1.346   97.619   89.932
LGA    N    38_A      N    38_A     0.327     0    0.055   0.617     2.769  100.000   88.929
LGA    A    39_A      A    39_A     0.028     0    0.022   0.038     0.154  100.000  100.000
LGA    E    40_A      E    40_A     0.168     0    0.042   0.191     0.451  100.000  100.000
LGA    N    41_A      N    41_A     0.285     0    0.023   0.138     0.989  100.000   97.619
LGA    V    42_A      V    42_A     0.481     0    0.031   1.157     3.278  100.000   87.619
LGA    E    43_A      E    43_A     0.183     0    0.069   0.212     1.320  100.000   94.762
LGA    G    44_A      G    44_A     0.141     0    0.015   0.015     0.151  100.000  100.000
LGA    K    45_A      K    45_A     0.219     0    0.031   0.739     4.524  100.000   77.566
LGA    R    46_A      R    46_A     0.361     0    0.017   0.299     1.487  100.000   92.338
LGA    G    47_A      G    47_A     0.273     0    0.012   0.012     0.273  100.000  100.000
LGA    L    48_A      L    48_A     0.350     0    0.037   0.057     0.565  100.000   98.810
LGA    I    49_A      I    49_A     0.293     0    0.035   0.063     0.325  100.000  100.000
LGA    H    50_A      H    50_A     0.377     0    0.010   0.115     0.799  100.000   95.238
LGA    V    51_A      V    51_A     0.085     0    0.032   0.052     0.148  100.000  100.000
LGA    V    52_A      V    52_A     0.361     0    0.019   0.046     0.609  100.000   95.918
LGA    L    53_A      L    53_A     0.516     0    0.029   0.086     1.219   97.619   91.786
LGA    V    54_A      V    54_A     0.243     0    0.065   0.082     0.420  100.000  100.000
LGA    E    55_A      E    55_A     0.102     0    0.020   0.212     0.650  100.000   98.942
LGA    K    56_A      K    56_A     0.068     0    0.025   0.581     1.747  100.000   95.926
LGA    Y    57_A      Y    57_A     0.166     0    0.575   0.563     2.457   91.190   90.119
LGA    G    58_A      G    58_A     2.035     0    0.148   0.148     2.715   62.976   62.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.048         12.985                 13.409           60.421   57.052

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.76    64.224    56.972     4.288

LGA_LOCAL      RMSD:   0.763  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.210  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.048  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.210503 * X  +  -0.785618 * Y  +  -0.581801 * Z  + -22.298840
  Y_new =  -0.550438 * X  +  -0.587081 * Y  +   0.593594 * Z  +  19.425957
  Z_new =  -0.807903 * X  +   0.195292 * Y  +  -0.556017 * Z  + -17.804213 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.205529  0.940584  2.803819   [DEG:  -69.0717   53.8915  160.6470 ]
ZXZ: -2.366227  2.160382 -1.333619   [DEG: -135.5748  123.7808  -76.4107 ]
 
# END of job
