
#######################################################
#                                                     #
#                        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 (  451),  selected   58 , name one
# Molecule2: number of CA atoms   83 (  623),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:E  -ch2:E  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      39_E - 65_E        4.70    16.51
  LONGEST_CONTINUOUS_SEGMENT:    27      40_E - 66_E        4.79    16.54
  LCS_AVERAGE:     26.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      41_E - 59_E        1.88    18.32
  LCS_AVERAGE:     14.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      42_E - 58_E        0.96    18.75
  LCS_AVERAGE:     12.82

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     K    24_E     K    24_E     11   12   18      8    9   11   12   13   13   13   13   14   14   15   16   17   18   20   20   22   24   26   27 
LCS_GDT     E    25_E     E    25_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   20   21   23   25   26   27 
LCS_GDT     L    26_E     L    26_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   20   21   23   25   26   27 
LCS_GDT     Q    27_E     Q    27_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   20   21   23   25   26   27 
LCS_GDT     L    28_E     L    28_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   21   21   23   25   26   27 
LCS_GDT     E    29_E     E    29_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   21   22   23   25   27   28 
LCS_GDT     L    30_E     L    30_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   21   22   23   25   27   28 
LCS_GDT     I    31_E     I    31_E     11   12   18      8    9   11   12   13   13   13   13   14   14   16   17   17   18   21   22   23   25   27   28 
LCS_GDT     K    32_E     K    32_E     11   12   18      4    9   11   12   13   13   13   13   14   14   16   17   17   18   21   22   23   25   27   28 
LCS_GDT     Q    33_E     Q    33_E     11   12   18      4    7   11   12   13   13   13   13   14   14   16   17   17   18   21   22   24   25   27   29 
LCS_GDT     F    34_E     F    34_E     11   12   18      4    4   11   12   13   13   13   13   14   14   15   16   17   18   21   21   23   25   27   29 
LCS_GDT     M    35_E     M    35_E      6   12   18      5    5    6   12   13   13   13   13   14   14   15   16   16   18   21   21   23   26   27   28 
LCS_GDT     A    36_E     A    36_E      6    6   18      5    5    6    6    6    6    9   10   14   14   16   20   21   24   26   30   30   32   35   38 
LCS_GDT     E    37_E     E    37_E      6    6   18      5    5    6    6    6    6    8   10   12   14   16   20   21   23   27   30   30   34   36   38 
LCS_GDT     A    38_E     A    38_E      6    6   22      5    5    6    9   13   13   13   13   14   14   15   16   16   19   21   25   27   28   32   33 
LCS_GDT     M    39_E     M    39_E      6    6   27      5    5    6    6    6    6    8   11   12   18   20   24   26   29   33   36   37   38   40   40 
LCS_GDT     K    40_E     K    40_E      6   13   27      3    4    6    7   10   13   15   18   20   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     I    41_E     I    41_E      4   19   27      3    5    5    9   13   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     G    42_E     G    42_E     17   19   27      3    6   13   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     N    43_E     N    43_E     17   19   27      5   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     K    44_E     K    44_E     17   19   27     12   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     E    45_E     E    45_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     G    46_E     G    46_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    47_E     L    47_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    48_E     L    48_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    49_E     L    49_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    50_E     L    50_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     A    51_E     A    51_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     E    52_E     E    52_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     R    53_E     R    53_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    54_E     L    54_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     E    55_E     E    55_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     A    56_E     A    56_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    57_E     L    57_E     17   19   27     12   16   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     K    58_E     K    58_E     17   19   27     13   16   17   18   18   19   19   21   22   23   23   25   27   28   32   35   37   38   40   40 
LCS_GDT     P    59_E     P    59_E      5   19   27      4    5    5    7   12   17   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     K    60_E     K    60_E      5    7   27      4    5    5    7    7    9    9   12   20   22   23   24   26   30   33   36   37   38   40   40 
LCS_GDT     V    61_E     V    61_E      5    7   27      4    5    5   10   14   17   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     S    62_E     S    62_E      5    7   27      3    5    5    7    7    9    9   10   12   14   18   24   27   28   32   36   37   38   40   40 
LCS_GDT     P    63_E     P    63_E      4    7   27      3    4    5    7    7    9    9   10   12   14   19   24   27   30   33   36   37   38   40   40 
LCS_GDT     E    64_E     E    64_E      4    7   27      3    4    5    7    7    9    9   11   12   14   19   25   27   30   33   36   37   38   40   40 
LCS_GDT     I    65_E     I    65_E      3    4   27      3    4    4    4    4    6    9   11   12   17   21   25   27   30   33   36   37   38   40   40 
LCS_GDT     A    66_E     A    66_E      6    6   27      4    5    6    6    6    9   13   16   19   20   21   24   26   30   33   36   37   38   40   40 
LCS_GDT     V    67_E     V    67_E      6    6   20      4    5    6    6    8    9   13   16   19   20   21   24   26   30   33   36   37   38   40   40 
LCS_GDT     L    68_E     L    68_E      6    6   16      4    5    6    6    9   12   14   16   19   20   21   24   26   29   33   36   37   38   40   40 
LCS_GDT     V    69_E     V    69_E      6    6   16      4    5    6    6    9   10   13   16   19   20   21   24   26   27   29   30   34   37   40   40 
LCS_GDT     E    70_E     E    70_E      6    6   16      3    5    6    6    6    7    9   11   15   18   21   23   25   26   27   30   30   35   40   40 
LCS_GDT     K    71_E     K    71_E      6    6   16      3    4    6    6    9   10   13   16   19   20   21   24   26   29   33   36   37   38   40   40 
LCS_GDT     A    72_E     A    72_E     10   10   16      4    9   10   10   10   10   10   12   17   20   21   24   26   28   33   36   37   38   40   40 
LCS_GDT     A    73_E     A    73_E     10   10   16      7    9   10   10   10   10   10   10   10   13   14   16   20   24   27   33   37   38   40   40 
LCS_GDT     E    74_E     E    74_E     10   10   16      7    9   10   10   10   10   10   10   11   13   21   24   26   30   33   36   37   38   40   40 
LCS_GDT     M    75_E     M    75_E     10   10   16      7    9   10   10   10   12   16   20   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    76_E     L    76_E     10   10   16      7    9   10   10   10   10   10   13   15   20   23   25   26   29   33   36   37   38   40   40 
LCS_GDT     K    77_E     K    77_E     10   10   16      7    9   10   10   10   10   10   13   19   20   21   25   26   30   33   36   37   38   40   40 
LCS_GDT     L    78_E     L    78_E     10   10   16      7    9   17   18   18   19   19   21   22   23   23   25   27   30   33   36   37   38   40   40 
LCS_GDT     L    79_E     L    79_E     10   10   16      7    9   10   10   10   16   18   19   19   20   22   24   26   27   27   28   31   32   38   39 
LCS_GDT     A    80_E     A    80_E     10   10   16      6    9   10   10   10   10   10   10   10   13   13   15   16   18   24   27   29   31   32   33 
LCS_GDT     K    81_E     K    81_E     10   10   16      4    9   10   10   10   10   10   10   15   16   17   20   22   25   26   30   30   32   35   36 
LCS_AVERAGE  LCS_A:  18.06  (  12.82   14.89   26.46 )

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     13     16     17     18     18     19     19     21     22     23     23     25     27     30     33     36     37     38     40     40 
GDT PERCENT_AT  15.66  19.28  20.48  21.69  21.69  22.89  22.89  25.30  26.51  27.71  27.71  30.12  32.53  36.14  39.76  43.37  44.58  45.78  48.19  48.19
GDT RMS_LOCAL    0.35   0.51   0.68   1.02   1.02   1.47   1.47   2.19   2.53   2.88   2.81   3.31   4.22   5.10   5.45   5.80   5.85   6.00   6.33   6.33
GDT RMS_ALL_AT  19.17  19.10  18.99  18.68  18.68  18.36  18.36  18.28  18.04  17.68  18.02  17.64  16.76  16.36  16.23  15.99  16.02  15.97  15.87  15.87

# Checking swapping
#   possible swapping detected:  E    25_E      E    25_E
#   possible swapping detected:  E    29_E      E    29_E
#   possible swapping detected:  E    37_E      E    37_E
#   possible swapping detected:  E    45_E      E    45_E
#   possible swapping detected:  E    64_E      E    64_E
#   possible swapping detected:  E    70_E      E    70_E
#   possible swapping detected:  E    74_E      E    74_E

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    24_E      K    24_E    41.702     0    0.230   1.031    44.060    0.000    0.000
LGA    E    25_E      E    25_E    44.536     0    0.034   0.456    52.755    0.000    0.000
LGA    L    26_E      L    26_E    40.493     0    0.069   0.141    41.977    0.000    0.000
LGA    Q    27_E      Q    27_E    35.417     0    0.032   1.235    37.454    0.000    0.000
LGA    L    28_E      L    28_E    37.769     0    0.037   1.401    40.418    0.000    0.000
LGA    E    29_E      E    29_E    38.208     0    0.077   0.794    43.267    0.000    0.000
LGA    L    30_E      L    30_E    32.842     0    0.042   0.985    34.846    0.000    0.000
LGA    I    31_E      I    31_E    30.620     0    0.045   0.128    32.264    0.000    0.000
LGA    K    32_E      K    32_E    33.384     0    0.036   1.017    42.237    0.000    0.000
LGA    Q    33_E      Q    33_E    30.603     0    0.036   0.768    33.156    0.000    0.000
LGA    F    34_E      F    34_E    26.402     0    0.539   1.482    28.015    0.000    0.000
LGA    M    35_E      M    35_E    25.409     0    0.644   0.596    30.103    0.000    0.000
LGA    A    36_E      A    36_E    22.082     0    0.036   0.041    23.890    0.000    0.000
LGA    E    37_E      E    37_E    18.416     0    0.053   1.087    21.792    0.000    0.000
LGA    A    38_E      A    38_E    17.670     0    0.067   0.065    20.020    0.000    0.000
LGA    M    39_E      M    39_E    14.262     0    0.667   0.766    18.874    0.000    0.000
LGA    K    40_E      K    40_E     7.751     0    0.723   1.077    10.331    8.452    8.148
LGA    I    41_E      I    41_E     4.702     0    0.581   0.790     6.985   27.857   29.583
LGA    G    42_E      G    42_E     2.422     0    0.124   0.124     2.630   64.881   64.881
LGA    N    43_E      N    43_E     0.856     0    0.220   0.892     4.762   90.476   75.595
LGA    K    44_E      K    44_E     1.453     0    0.056   1.110     4.537   81.429   64.497
LGA    E    45_E      E    45_E     1.458     0    0.054   0.755     3.099   81.429   68.889
LGA    G    46_E      G    46_E     0.803     0    0.038   0.038     1.115   90.595   90.595
LGA    L    47_E      L    47_E     0.874     0    0.038   0.906     3.907   88.214   73.988
LGA    L    48_E      L    48_E     1.206     0    0.035   1.011     4.738   81.429   69.107
LGA    L    49_E      L    49_E     0.871     0    0.035   1.018     4.503   88.214   75.536
LGA    L    50_E      L    50_E     0.794     0    0.056   0.130     1.198   90.476   89.345
LGA    A    51_E      A    51_E     1.335     0    0.025   0.042     1.573   81.429   79.714
LGA    E    52_E      E    52_E     0.926     0    0.037   1.017     4.763   88.214   66.614
LGA    R    53_E      R    53_E     0.746     0    0.064   1.110     3.530   85.952   68.745
LGA    L    54_E      L    54_E     1.569     0    0.033   1.229     4.781   75.000   65.774
LGA    E    55_E      E    55_E     1.637     0    0.057   0.768     3.449   72.857   66.032
LGA    A    56_E      A    56_E     1.551     0    0.147   0.146     1.648   75.000   76.286
LGA    L    57_E      L    57_E     2.242     0    0.225   0.239     3.022   61.071   62.917
LGA    K    58_E      K    58_E     2.179     0    0.610   1.151    12.554   63.095   35.291
LGA    P    59_E      P    59_E     3.982     0    0.054   0.140     7.376   38.095   49.252
LGA    K    60_E      K    60_E     7.136     0    0.191   0.788    15.569   11.905    5.873
LGA    V    61_E      V    61_E     4.854     0    0.123   1.169     6.712   23.333   40.408
LGA    S    62_E      S    62_E     8.975     0    0.073   0.105    12.183    7.738    5.159
LGA    P    63_E      P    63_E    10.715     0    0.694   0.614    13.180    0.000    0.000
LGA    E    64_E      E    64_E    11.221     0    0.664   0.715    11.719    0.000    0.000
LGA    I    65_E      I    65_E    11.308     0    0.642   0.829    14.735    0.000    0.000
LGA    A    66_E      A    66_E    14.831     0    0.631   0.578    17.040    0.000    0.000
LGA    V    67_E      V    67_E    15.645     0    0.037   0.943    18.009    0.000    0.000
LGA    L    68_E      L    68_E    15.070     0    0.031   1.213    15.903    0.000    0.000
LGA    V    69_E      V    69_E    16.301     0    0.053   1.005    17.707    0.000    0.000
LGA    E    70_E      E    70_E    18.071     0    0.596   0.965    20.859    0.000    0.000
LGA    K    71_E      K    71_E    15.393     0    0.063   0.916    19.580    0.000    0.000
LGA    A    72_E      A    72_E    14.141     0    0.614   0.581    14.828    0.000    0.000
LGA    A    73_E      A    73_E    14.776     0    0.036   0.059    17.380    0.000    0.000
LGA    E    74_E      E    74_E    11.962     0    0.097   1.057    19.384    2.857    1.270
LGA    M    75_E      M    75_E     6.787     0    0.029   0.823     9.131   25.833   20.357
LGA    L    76_E      L    76_E     6.678     0    0.044   1.035    12.659   14.286    7.560
LGA    K    77_E      K    77_E     7.480     0    0.023   0.922    14.508   19.405    8.942
LGA    L    78_E      L    78_E     1.825     0    0.105   1.021     6.754   51.071   37.976
LGA    L    79_E      L    79_E     5.746     0    0.026   1.252     9.945   19.762   24.345
LGA    A    80_E      A    80_E    10.789     0    0.070   0.067    13.246    1.190    0.952
LGA    K    81_E      K    81_E     9.416     0    0.112   1.177    10.983    0.833    4.444

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     451    451  100.00                83
SUMMARY(RMSD_GDC):    13.046         12.819                 14.011           19.426   17.326

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   83    4.0     21    2.19    27.410    23.191     0.918

LGA_LOCAL      RMSD:   2.187  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.281  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.046  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.581024 * X  +   0.220062 * Y  +   0.783571 * Z  + -58.413082
  Y_new =   0.352332 * X  +   0.935874 * Y  +  -0.001579 * Z  + -53.812778
  Z_new =  -0.733671 * X  +   0.275160 * Y  +  -0.621300 * Z  +   1.026918 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.596482  0.823708  2.724678   [DEG:  148.7675   47.1950  156.1125 ]
ZXZ:  1.568782  2.241198 -1.211986   [DEG:   89.8846  128.4112  -69.4417 ]
 
# END of job
