
#######################################################
#                                                     #
#                        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        4.35    14.91
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.60    15.10
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      35_A - 57_A        0.46    15.10
  LCS_AVERAGE:     28.15

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      0    3    3    6   24   30   33   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     20   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     24   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     20   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     20   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     20   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      4   14   33   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      4    6   24   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      6   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    7   13   16   25   35   36   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     10   14   14   15   15   15   20   21   28   34   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   23   26   31   38   41   43   46   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   27   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25      4   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25      6   14   14   15   15   15   16   18   20   22   22   22   22   27   29   30   34   35   39   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    6   10   15   15   15   16   18   20   22   24   26   28   30   40   44   45   46   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    4    7   10   15   18   20   22   24   28   36   41   42   44   45   46   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    8   11   16   18   20   22   36   39   40   42   43   44   45   46   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    8    9   17   21   32   38   39   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    34_A     E    34_A      3   25   29      3    3    4   10   16   23   30   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     Q    35_A     Q    35_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     L    36_A     L    36_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     W    37_A     W    37_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     N    38_A     N    38_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     A    39_A     A    39_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    40_A     E    40_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     N    41_A     N    41_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     V    42_A     V    42_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    43_A     E    43_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     G    44_A     G    44_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     K    45_A     K    45_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     R    46_A     R    46_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     G    47_A     G    47_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     L    48_A     L    48_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     I    49_A     I    49_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     H    50_A     H    50_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     V    51_A     V    51_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     V    52_A     V    52_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     L    53_A     L    53_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     V    54_A     V    54_A     23   25   29     14   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     E    55_A     E    55_A     23   25   29     25   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     K    56_A     K    56_A     23   25   29     20   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     Y    57_A     Y    57_A     23   25   29      6   33   34   36   36   36   36   37   38   39   40   41   42   42   43   44   45   46   46   46 
LCS_GDT     G    58_A     G    58_A      3   25   29      3    3    4    8   11   27   36   37   38   38   40   41   42   42   43   44   45   46   46   46 
LCS_AVERAGE  LCS_A:  34.94  (  28.15   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     25     33     34     36     36     36     36     37     38     39     40     41     42     42     43     44     45     46     46     46 
GDT PERCENT_AT  43.10  56.90  58.62  62.07  62.07  62.07  62.07  63.79  65.52  67.24  68.97  70.69  72.41  72.41  74.14  75.86  77.59  79.31  79.31  79.31
GDT RMS_LOCAL    0.33   0.46   0.50   0.77   0.77   0.77   0.77   1.20   1.49   1.87   2.24   2.40   2.76   2.76   3.16   3.58   4.02   4.32   4.32   4.32
GDT RMS_ALL_AT  15.12  15.12  15.11  15.14  15.14  15.14  15.14  15.11  15.08  15.02  14.91  14.88  14.86  14.86  14.82  14.74  14.63  14.52  14.52  14.52

# Checking swapping
#   possible swapping detected:  D     9_A      D     9_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    33_A      E    33_A
#   possible swapping detected:  E    55_A      E    55_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.498     0    0.435   0.489     8.275   28.810   24.000
LGA    E     2_A      E     2_A     0.776     0    0.654   1.452     7.419   84.524   50.952
LGA    Y     3_A      Y     3_A     0.478     0    0.061   1.368     8.678   95.238   58.254
LGA    V     4_A      V     4_A     0.501     0    0.047   0.131     0.607   95.238   94.558
LGA    R     5_A      R     5_A     0.486     0    0.074   0.643     4.549   95.238   78.139
LGA    A     6_A      A     6_A     0.603     0    0.041   0.043     0.690   90.476   92.381
LGA    L     7_A      L     7_A     0.741     0    0.084   1.041     2.940   88.214   83.155
LGA    F     8_A      F     8_A     0.680     0    0.069   0.294     1.902   90.476   85.628
LGA    D     9_A      D     9_A     0.607     0    0.047   1.089     4.656   92.857   75.060
LGA    H    10_A      H    10_A     0.576     0    0.034   1.143     2.699   90.476   82.810
LGA    T    11_A      T    11_A     0.565     0    0.101   0.196     1.190   90.595   87.959
LGA    G    12_A      G    12_A     2.016     0    0.032   0.032     2.016   75.119   75.119
LGA    H    13_A      H    13_A     2.686     0    0.597   0.589     4.170   54.048   56.667
LGA    D    14_A      D    14_A     1.086     0    0.048   1.106     5.473   61.071   50.476
LGA    E    15_A      E    15_A     7.225     0    0.631   1.083    12.540   13.333    6.296
LGA    Q    16_A      Q    16_A     8.701     0    0.639   1.056    13.962    2.619    1.481
LGA    E    17_A      E    17_A    12.240     0    0.113   1.201    15.840    0.000    0.000
LGA    L    18_A      L    18_A    19.360     0    0.083   0.779    23.461    0.000    0.000
LGA    P    19_A      P    19_A    24.858     0    0.024   0.142    27.625    0.000    0.000
LGA    F    20_A      F    20_A    30.678     0    0.027   1.406    32.803    0.000    0.000
LGA    K    21_A      K    21_A    37.445     0    0.047   1.310    44.395    0.000    0.000
LGA    K    22_A      K    22_A    40.072     0    0.039   1.092    47.234    0.000    0.000
LGA    G    23_A      G    23_A    42.162     0    0.068   0.068    42.412    0.000    0.000
LGA    E    24_A      E    24_A    38.724     0    0.035   1.036    39.368    0.000    0.000
LGA    I    25_A      I    25_A    36.554     0    0.045   0.633    41.298    0.000    0.000
LGA    L    26_A      L    26_A    30.249     0    0.082   0.186    32.217    0.000    0.000
LGA    R    27_A      R    27_A    28.020     0    0.067   1.134    33.562    0.000    0.000
LGA    I    28_A      I    28_A    20.882     0    0.036   0.144    23.648    0.000    0.000
LGA    R    29_A      R    29_A    20.173     0    0.065   0.924    30.149    0.000    0.000
LGA    D    30_A      D    30_A    16.240     0    0.587   1.216    20.799    0.000    0.000
LGA    K    31_A      K    31_A    14.196     0    0.259   0.349    21.651    0.000    0.000
LGA    P    32_A      P    32_A    12.746     0    0.066   0.072    15.856    0.000    0.000
LGA    E    33_A      E    33_A    10.336     0    0.724   1.200    14.812    1.905    0.847
LGA    E    34_A      E    34_A     5.918     0    0.227   0.901     8.333   27.381   17.778
LGA    Q    35_A      Q    35_A     0.986     0    0.608   1.050     6.820   86.071   53.862
LGA    L    36_A      L    36_A     0.874     0    0.040   0.794     2.474   88.214   83.929
LGA    W    37_A      W    37_A     0.661     0    0.037   0.301     1.810   95.238   88.027
LGA    N    38_A      N    38_A     0.622     0    0.034   0.733     3.027   90.476   80.000
LGA    A    39_A      A    39_A     0.319     0    0.039   0.047     0.463  100.000  100.000
LGA    E    40_A      E    40_A     0.159     0    0.021   0.592     1.792  100.000   94.921
LGA    N    41_A      N    41_A     0.378     0    0.035   0.342     1.288   97.619   95.298
LGA    V    42_A      V    42_A     0.749     0    0.029   0.106     1.393   90.476   86.599
LGA    E    43_A      E    43_A     0.213     0    0.261   0.224     3.455   95.357   77.778
LGA    G    44_A      G    44_A     0.267     0    0.092   0.092     0.470  100.000  100.000
LGA    K    45_A      K    45_A     0.406     0    0.040   0.695     3.253  100.000   92.328
LGA    R    46_A      R    46_A     0.239     0    0.050   0.867     2.068  100.000   89.957
LGA    G    47_A      G    47_A     0.288     0    0.046   0.046     0.384  100.000  100.000
LGA    L    48_A      L    48_A     0.487     0    0.048   0.193     1.135   95.238   91.726
LGA    I    49_A      I    49_A     0.712     0    0.041   0.089     1.367   90.476   87.083
LGA    H    50_A      H    50_A     0.613     0    0.061   0.234     1.757   90.476   86.095
LGA    V    51_A      V    51_A     0.702     0    0.020   0.094     0.840   90.476   90.476
LGA    V    52_A      V    52_A     0.479     0    0.100   1.075     2.510   92.857   84.558
LGA    L    53_A      L    53_A     0.622     0    0.107   0.979     3.047   92.857   84.405
LGA    V    54_A      V    54_A     0.994     0    0.054   0.141     1.082   88.214   86.599
LGA    E    55_A      E    55_A     0.616     0    0.035   0.743     2.861   95.238   77.778
LGA    K    56_A      K    56_A     0.409     0    0.122   1.124     5.343   97.619   82.804
LGA    Y    57_A      Y    57_A     0.782     0    0.583   0.493     2.133   86.071   82.421
LGA    G    58_A      G    58_A     5.341     0    0.371   0.371     9.599   17.738   17.738

# 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):    13.067         12.992                 13.452           57.902   52.344

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    1.20    64.655    56.677     2.856

LGA_LOCAL      RMSD:   1.195  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.109  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.067  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.338462 * X  +   0.939956 * Y  +  -0.043899 * Z  + -38.095570
  Y_new =  -0.903302 * X  +  -0.337625 * Y  +  -0.264678 * Z  +  48.904591
  Z_new =  -0.263607 * X  +  -0.049929 * Y  +   0.963337 * Z  + -42.544506 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.929298  0.266760 -0.051783   [DEG: -110.5407   15.2842   -2.9669 ]
ZXZ: -0.164363  0.271621 -1.757985   [DEG:   -9.4173   15.5628 -100.7251 ]
 
# END of job
