
#######################################################
#                                                     #
#                        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   54 (  451),  selected   54 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   54 , 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:    44      13_A - 56_A        4.97    13.72
  LCS_AVERAGE:     66.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      31_A - 56_A        1.79    14.29
  LCS_AVERAGE:     34.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      33_A - 56_A        0.98    14.42
  LCS_AVERAGE:     30.59

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   54
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     Y     3_A     Y     3_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     V     4_A     V     4_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     R     5_A     R     5_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     A     6_A     A     6_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     L     7_A     L     7_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     F     8_A     F     8_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     D     9_A     D     9_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     H    10_A     H    10_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     T    11_A     T    11_A     12   13   15      9   10   11   12   12   13   13   14   15   15   15   17   17   17   19   19   20   22   22   24 
LCS_GDT     G    12_A     G    12_A     12   13   19      7   10   11   12   12   13   13   14   15   15   15   17   17   17   19   20   22   22   25   29 
LCS_GDT     H    13_A     H    13_A     12   13   44      5    8   11   12   12   13   13   14   15   15   15   19   24   29   31   33   35   39   40   43 
LCS_GDT     D    14_A     D    14_A     12   13   44      3    9   11   12   12   13   16   23   24   28   30   33   36   40   43   43   43   43   43   43 
LCS_GDT     E    15_A     E    15_A      3   16   44      3    3    4    5    6   12   20   22   25   29   34   35   41   42   43   43   43   43   43   43 
LCS_GDT     Q    16_A     Q    16_A     15   16   44      3   14   15   17   18   21   24   26   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    17_A     E    17_A     15   16   44      5   14   15   17   18   21   24   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     L    18_A     L    18_A     15   16   44      5   14   15   17   18   21   24   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     P    19_A     P    19_A     15   16   44      9   14   15   17   18   21   27   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     F    20_A     F    20_A     15   16   44      9   14   15   20   23   25   27   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     K    21_A     K    21_A     15   16   44      9   14   15   17   18   25   27   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     K    22_A     K    22_A     15   16   44      9   14   15   17   18   21   24   28   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     G    23_A     G    23_A     15   16   44      9   14   15   20   25   25   26   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    24_A     E    24_A     15   16   44      9   14   24   24   25   26   27   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     I    25_A     I    25_A     15   16   44      9   22   24   25   25   26   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     L    26_A     L    26_A     15   16   44      9   14   23   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     R    27_A     R    27_A     15   16   44      9   14   15   17   26   27   28   29   30   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     I    28_A     I    28_A     15   16   44      5   14   15   17   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     R    29_A     R    29_A     15   16   44      5   14   15   17   18   21   25   28   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     D    30_A     D    30_A     15   16   44      5    9   15   17   18   21   24   26   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     K    31_A     K    31_A      5   26   44      3    4    6   10   23   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     P    32_A     P    32_A      5   26   44      3    4    6    7    9   13   17   24   30   31   33   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    33_A     E    33_A     24   26   44      3    4    6   10   21   25   27   29   31   33   35   37   41   42   43   43   43   43   43   43 
LCS_GDT     E    34_A     E    34_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     Q    35_A     Q    35_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     L    36_A     L    36_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     W    37_A     W    37_A     24   26   44      6   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     N    38_A     N    38_A     24   26   44     10   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     A    39_A     A    39_A     24   26   44     10   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    40_A     E    40_A     24   26   44     11   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     N    41_A     N    41_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     V    42_A     V    42_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    43_A     E    43_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     G    44_A     G    44_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     K    45_A     K    45_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     R    46_A     R    46_A     24   26   44     10   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     G    47_A     G    47_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     L    48_A     L    48_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     I    49_A     I    49_A     24   26   44      6   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     H    50_A     H    50_A     24   26   44      9   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     V    51_A     V    51_A     24   26   44     11   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     V    52_A     V    52_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     L    53_A     L    53_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     V    54_A     V    54_A     24   26   44      5   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     E    55_A     E    55_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_GDT     K    56_A     K    56_A     24   26   44     14   22   24   25   26   27   28   29   32   35   38   39   41   42   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  44.02  (  30.59   34.74   66.73 )

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     14     22     24     25     26     27     28     29     32     35     38     39     41     42     43     43     43     43     43     43 
GDT PERCENT_AT  24.14  37.93  41.38  43.10  44.83  46.55  48.28  50.00  55.17  60.34  65.52  67.24  70.69  72.41  74.14  74.14  74.14  74.14  74.14  74.14
GDT RMS_LOCAL    0.37   0.57   0.66   0.82   1.50   1.66   1.70   1.86   2.65   3.02   3.50   3.59   3.78   4.00   4.31   4.31   4.31   4.31   4.31   4.31
GDT RMS_ALL_AT  14.54  14.54  14.62  14.65  14.83  14.77  14.71  14.68  14.21  14.16  14.12  14.12  14.03  13.95  13.85  13.85  13.85  13.85  13.85  13.85

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D     9_A      D     9_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    55_A      E    55_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     3_A      Y     3_A    30.864     0    0.040   0.241    39.692    0.000    0.000
LGA    V     4_A      V     4_A    27.828     0    0.053   0.075    30.888    0.000    0.000
LGA    R     5_A      R     5_A    31.630     0    0.015   1.210    42.913    0.000    0.000
LGA    A     6_A      A     6_A    30.312     0    0.056   0.057    34.333    0.000    0.000
LGA    L     7_A      L     7_A    32.263     0    0.029   0.096    35.779    0.000    0.000
LGA    F     8_A      F     8_A    34.371     0    0.063   1.306    34.371    0.000    0.000
LGA    D     9_A      D     9_A    35.514     0    0.042   0.983    41.666    0.000    0.000
LGA    H    10_A      H    10_A    29.697     0    0.036   1.285    31.740    0.000    0.000
LGA    T    11_A      T    11_A    30.413     0    0.053   0.106    35.080    0.000    0.000
LGA    G    12_A      G    12_A    24.021     0    0.116   0.116    26.609    0.000    0.000
LGA    H    13_A      H    13_A    22.647     0    0.632   1.205    25.174    0.000    0.000
LGA    D    14_A      D    14_A    17.033     0    0.062   1.020    19.137    0.000    0.000
LGA    E    15_A      E    15_A    13.900     0    0.683   1.161    18.692    0.000    0.000
LGA    Q    16_A      Q    16_A     9.881     0    0.664   1.493    16.652    1.667    0.741
LGA    E    17_A      E    17_A     8.878     0    0.135   0.323     9.463    1.786    1.746
LGA    L    18_A      L    18_A     9.146     0    0.025   1.300     9.814    1.190    3.571
LGA    P    19_A      P    19_A    11.585     0    0.048   0.076    13.024    0.119    0.068
LGA    F    20_A      F    20_A    10.234     0    0.040   1.367    12.035    0.000   10.433
LGA    K    21_A      K    21_A    11.658     0    0.023   0.082    16.999    0.119    0.053
LGA    K    22_A      K    22_A    12.039     0    0.078   0.682    15.071    0.000    0.000
LGA    G    23_A      G    23_A     9.192     0    0.012   0.012    10.169    5.476    5.476
LGA    E    24_A      E    24_A     6.190     0    0.065   0.189     8.791   21.190   15.344
LGA    I    25_A      I    25_A     2.257     0    0.039   0.075     3.620   61.429   68.274
LGA    L    26_A      L    26_A     0.845     0    0.053   0.115     3.983   77.381   66.845
LGA    R    27_A      R    27_A     3.950     0    0.038   1.295    11.032   48.452   23.074
LGA    I    28_A      I    28_A     4.086     0    0.033   0.157     6.005   29.405   35.833
LGA    R    29_A      R    29_A     5.873     0    0.619   1.339    14.449   20.000   11.732
LGA    D    30_A      D    30_A     7.234     0    0.217   1.045    11.111   16.429    8.274
LGA    K    31_A      K    31_A     3.951     0    0.062   1.082    10.479   33.333   21.852
LGA    P    32_A      P    32_A     5.790     0    0.356   0.571     7.610   23.810   19.592
LGA    E    33_A      E    33_A     4.263     0    0.131   1.159     5.002   38.929   41.376
LGA    E    34_A      E    34_A     1.337     0    0.434   1.026     7.667   77.143   53.968
LGA    Q    35_A      Q    35_A     1.104     0    0.070   1.265     5.465   85.952   69.259
LGA    L    36_A      L    36_A     0.986     0    0.025   0.630     1.909   83.690   80.417
LGA    W    37_A      W    37_A     1.695     0    0.082   0.175     2.475   75.000   68.265
LGA    N    38_A      N    38_A     1.418     0    0.051   0.579     2.995   79.286   73.155
LGA    A    39_A      A    39_A     1.100     0    0.020   0.041     1.273   85.952   85.048
LGA    E    40_A      E    40_A     0.492     0    0.016   0.399     1.166   92.857   90.529
LGA    N    41_A      N    41_A     0.785     0    0.018   0.114     1.119   92.857   89.405
LGA    V    42_A      V    42_A     1.459     0    0.039   1.149     3.373   77.143   73.265
LGA    E    43_A      E    43_A     1.612     0    0.034   0.845     3.295   77.143   69.524
LGA    G    44_A      G    44_A     0.693     0    0.039   0.039     0.967   90.476   90.476
LGA    K    45_A      K    45_A     1.067     0    0.043   0.683     4.582   90.595   76.190
LGA    R    46_A      R    46_A     1.017     0    0.017   1.299     6.849   81.429   57.835
LGA    G    47_A      G    47_A     1.106     0    0.019   0.019     1.106   85.952   85.952
LGA    L    48_A      L    48_A     1.209     0    0.056   0.088     2.729   79.286   72.083
LGA    I    49_A      I    49_A     0.766     0    0.022   1.176     4.928   90.476   72.857
LGA    H    50_A      H    50_A     0.732     0    0.010   1.222     6.204   95.238   64.810
LGA    V    51_A      V    51_A     0.343     0    0.075   1.174     2.616   95.238   84.762
LGA    V    52_A      V    52_A     1.141     0    0.023   0.076     1.678   85.952   82.789
LGA    L    53_A      L    53_A     0.658     0    0.029   0.074     0.991   90.476   90.476
LGA    V    54_A      V    54_A     0.844     0    0.124   1.190     2.844   88.214   80.748
LGA    E    55_A      E    55_A     1.432     0    0.060   0.724     1.865   81.429   79.524
LGA    K    56_A      K    56_A     1.266     0    0.150   0.834     4.511   83.690   68.942

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       54     216    216  100.00     451    451  100.00                58
SUMMARY(RMSD_GDC):    12.663         12.591                 13.714           40.452   36.113

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   54   58    4.0     29    1.86    51.293    48.188     1.480

LGA_LOCAL      RMSD:   1.859  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.678  Number of assigned atoms:   54 
Std_ASGN_ATOMS RMSD:  12.663  Standard rmsd on all 54 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.923863 * X  +   0.245216 * Y  +  -0.293848 * Z  + -35.119675
  Y_new =  -0.368330 * X  +  -0.778249 * Y  +   0.508587 * Z  +  53.782967
  Z_new =  -0.103974 * X  +   0.578098 * Y  +   0.809316 * Z  + -35.918076 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.762220  0.104162  0.620261   [DEG: -158.2636    5.9680   35.5384 ]
ZXZ: -2.617676  0.627809 -0.177952   [DEG: -149.9818   35.9708  -10.1959 ]
 
# END of job
