
#######################################################
#                                                     #
#                        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        4.51    14.85
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.49    15.10
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.77    15.10
  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    4    9   22   29   36   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     26   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     23   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     26   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   17   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    5   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    4    6   15   21   31   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      6   14   14   14   15   15   25   25   30   36   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     11   14   14   14   15   15   16   18   21   22   22   22   26   32   36   40   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   32   37   38 
LCS_GDT     P    19_A     P    19_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   24   27   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   25   29   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   29   32   34   37   38 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    3    8   14   15   15   16   18   21   22   22   22   28   32   34   38   45   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   11   15   18   21   22   23   23   28   41   43   44   45   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   12   16   18   21   22   22   22   32   42   43   44   45   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    6    9   12   28   33   39   40   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    3    5    5    5   20   25   37   38   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      5   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     29   34   36   36   36   36   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    6   28   34   35   37   37   39   40   41   42   42   42   43   44   45   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     29     34     36     36     36     36     37     37     39     40     41     42     42     42     43     44     45     45     46     46 
GDT PERCENT_AT  50.00  58.62  62.07  62.07  62.07  62.07  63.79  63.79  67.24  68.97  70.69  72.41  72.41  72.41  74.14  75.86  77.59  77.59  79.31  79.31
GDT RMS_LOCAL    0.25   0.36   0.61   0.61   0.61   0.61   0.86   0.86   1.76   2.00   2.32   2.70   2.70   2.70   3.16   3.60   4.06   3.95   4.35   4.35
GDT RMS_ALL_AT  15.11  15.13  15.16  15.16  15.16  15.16  15.14  15.14  14.99  14.96  14.86  14.83  14.83  14.83  14.79  14.70  14.58  14.58  14.47  14.47

# 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    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    34_A      E    34_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.225     0    0.439   0.464     8.791   17.619   15.048
LGA    E     2_A      E     2_A     0.445     0    0.618   1.152     6.330   87.500   56.561
LGA    Y     3_A      Y     3_A     0.260     0    0.000   0.111     1.315  100.000   93.770
LGA    V     4_A      V     4_A     0.365     0    0.041   0.067     0.458  100.000  100.000
LGA    R     5_A      R     5_A     0.434     0    0.073   1.137     3.364  100.000   86.537
LGA    A     6_A      A     6_A     0.521     0    0.035   0.055     0.654   90.476   90.476
LGA    L     7_A      L     7_A     0.540     0    0.070   1.179     3.613   92.857   83.571
LGA    F     8_A      F     8_A     0.503     0    0.037   0.127     0.559   95.238   97.403
LGA    D     9_A      D     9_A     0.585     0    0.000   0.674     1.746   90.476   86.071
LGA    H    10_A      H    10_A     0.652     0    0.050   1.075     2.208   90.476   82.667
LGA    T    11_A      T    11_A     0.592     0    0.150   0.233     1.857   88.214   84.082
LGA    G    12_A      G    12_A     1.983     0    0.000   0.000     1.983   83.929   83.929
LGA    H    13_A      H    13_A     2.074     0    0.664   1.495     5.454   57.857   48.619
LGA    D    14_A      D    14_A     0.823     0    0.031   1.041     5.686   65.595   52.857
LGA    E    15_A      E    15_A     7.031     0    0.670   0.915    13.126   16.071    7.513
LGA    Q    16_A      Q    16_A     8.537     0    0.678   1.024    10.558    2.619    2.116
LGA    E    17_A      E    17_A    12.050     0    0.054   0.872    15.824    0.000    0.000
LGA    L    18_A      L    18_A    19.183     0    0.085   1.020    22.955    0.000    0.000
LGA    P    19_A      P    19_A    24.599     0    0.000   0.104    27.362    0.000    0.000
LGA    F    20_A      F    20_A    30.400     0    0.000   1.442    32.520    0.000    0.000
LGA    K    21_A      K    21_A    37.157     0    0.000   0.734    39.613    0.000    0.000
LGA    K    22_A      K    22_A    40.280     0    0.000   0.453    48.557    0.000    0.000
LGA    G    23_A      G    23_A    42.298     0    0.000   0.000    42.300    0.000    0.000
LGA    E    24_A      E    24_A    38.643     0    0.020   1.060    39.448    0.000    0.000
LGA    I    25_A      I    25_A    36.349     0    0.065   0.609    41.175    0.000    0.000
LGA    L    26_A      L    26_A    29.975     0    0.074   0.073    31.984    0.000    0.000
LGA    R    27_A      R    27_A    28.247     0    0.061   0.130    32.442    0.000    0.000
LGA    I    28_A      I    28_A    21.204     0    0.032   0.046    23.937    0.000    0.000
LGA    R    29_A      R    29_A    20.973     0    0.638   1.178    27.918    0.000    0.000
LGA    D    30_A      D    30_A    16.988     0    0.664   1.082    20.812    0.000    0.000
LGA    K    31_A      K    31_A    14.971     0    0.311   0.343    21.883    0.000    0.000
LGA    P    32_A      P    32_A    13.695     0    0.143   0.397    16.074    0.000    0.000
LGA    E    33_A      E    33_A    10.710     0    0.699   1.055    13.328    0.476    0.212
LGA    E    34_A      E    34_A     6.823     0    0.208   0.978     8.126   19.048   14.974
LGA    Q    35_A      Q    35_A     0.882     0    0.655   1.233     5.135   84.524   63.175
LGA    L    36_A      L    36_A     0.532     0    0.134   0.740     1.688   90.595   86.131
LGA    W    37_A      W    37_A     0.428     0    0.000   0.234     1.487  100.000   90.646
LGA    N    38_A      N    38_A     0.489     0    0.000   0.905     2.991   97.619   85.536
LGA    A    39_A      A    39_A     0.098     0    0.030   0.045     0.432  100.000  100.000
LGA    E    40_A      E    40_A     0.047     0    0.000   0.187     0.903  100.000   97.884
LGA    N    41_A      N    41_A     0.041     0    0.058   0.210     1.044  100.000   97.679
LGA    V    42_A      V    42_A     0.199     0    0.000   0.000     0.535  100.000   98.639
LGA    E    43_A      E    43_A     0.159     0    0.073   0.333     1.233  100.000   94.815
LGA    G    44_A      G    44_A     0.247     0    0.057   0.057     0.346  100.000  100.000
LGA    K    45_A      K    45_A     0.278     0    0.061   1.174     4.365  100.000   78.889
LGA    R    46_A      R    46_A     0.143     0    0.043   0.098     0.368  100.000  100.000
LGA    G    47_A      G    47_A     0.188     0    0.046   0.046     0.212  100.000  100.000
LGA    L    48_A      L    48_A     0.294     0    0.043   0.227     1.006  100.000   95.298
LGA    I    49_A      I    49_A     0.397     0    0.061   0.088     0.487  100.000  100.000
LGA    H    50_A      H    50_A     0.443     0    0.000   1.115     4.826  100.000   77.667
LGA    V    51_A      V    51_A     0.383     0    0.000   0.006     0.503  100.000   98.639
LGA    V    52_A      V    52_A     0.287     0    0.000   1.090     2.665  100.000   90.000
LGA    L    53_A      L    53_A     0.293     0    0.042   0.041     0.654  100.000   96.429
LGA    V    54_A      V    54_A     0.280     0    0.000   0.082     0.425  100.000  100.000
LGA    E    55_A      E    55_A     0.171     0    0.040   0.182     0.760  100.000   97.884
LGA    K    56_A      K    56_A     0.301     0    0.042   0.903     3.767   97.619   81.376
LGA    Y    57_A      Y    57_A     0.559     0    0.198   0.375     2.960   81.786   71.270
LGA    G    58_A      G    58_A     3.565     0    0.410   0.410     4.444   45.595   45.595

# 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):    12.995         12.916                 13.347           60.279   55.758

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.86    65.086    57.441     3.868

LGA_LOCAL      RMSD:   0.857  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.142  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  12.995  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.410132 * X  +   0.895319 * Y  +   0.173771 * Z  + 170.468140
  Y_new =   0.889611 * X  +   0.350742 * Y  +   0.292527 * Z  + -389.822235
  Z_new =   0.200956 * X  +   0.274563 * Y  +  -0.940336 * Z  + -119.557472 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.002780 -0.202334  2.857507   [DEG:  114.7508  -11.5929  163.7231 ]
ZXZ:  2.605572  2.794413  0.631824   [DEG:  149.2883  160.1081   36.2009 ]
 
# END of job
