
#######################################################
#                                                     #
#                        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        1.53    15.10
  LCS_AVERAGE:     33.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.85    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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     27   34   35   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     24   34   35   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     27   34   35   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   14   31   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   14   35   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   17   25     30   34   35   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   17   25      3    3    4    6    8   20   30   36   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   17   25      9   14   14   14   15   15   22   25   30   36   41   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   17   25     11   14   14   14   15   15   16   18   21   22   22   22   26   32   36   41   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   17   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   17   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   17   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   17   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   17   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   17   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   17   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   17   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   17   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   17   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   17   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   25   29   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   16   18   21   22   22   22   22   23   24   29   32   34   37   42 
LCS_GDT     D    30_A     D    30_A     15   17   29      3    3    8   14   15   15   16   18   21   22   22   22   28   32   34   35   45   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   11   16   18   21   22   23   24   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   33   42   43   44   45   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    5    6    7    9   14   28   33   38   40   42   42   42   43   44   45   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    5   19   26   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   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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     30   34   35   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    8   33   35   37   37   39   40   41   42   42   42   43   44   45   45   46   46 
LCS_AVERAGE  LCS_A:  35.57  (  29.49   33.38   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     34     35     36     36     36     37     37     39     40     41     42     42     42     43     44     45     45     46     46 
GDT PERCENT_AT  51.72  58.62  60.34  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    0.26   0.35   0.52   0.63   0.63   0.63   0.93   0.93   1.80   2.04   2.36   2.72   2.72   2.72   3.18   3.61   4.07   3.96   4.36   4.36
GDT RMS_ALL_AT  15.12  15.13  15.15  15.17  15.17  15.17  15.14  15.14  14.99  14.96  14.86  14.83  14.83  14.83  14.78  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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.333     0    0.262   0.282     9.012   17.262   14.762
LGA    E     2_A      E     2_A     0.451     0    0.618   1.142     6.341   87.500   56.561
LGA    Y     3_A      Y     3_A     0.307     0    0.031   0.113     1.270  100.000   95.278
LGA    V     4_A      V     4_A     0.402     0    0.065   0.073     0.487  100.000  100.000
LGA    R     5_A      R     5_A     0.459     0    0.049   1.115     3.376  100.000   86.537
LGA    A     6_A      A     6_A     0.545     0    0.000   0.000     0.659   90.476   90.476
LGA    L     7_A      L     7_A     0.566     0    0.000   0.069     0.957   90.476   90.476
LGA    F     8_A      F     8_A     0.515     0    0.000   0.113     0.620   95.238   95.671
LGA    D     9_A      D     9_A     0.588     0    0.048   0.700     1.754   92.857   87.262
LGA    H    10_A      H    10_A     0.633     0    0.062   1.121     2.332   90.476   83.524
LGA    T    11_A      T    11_A     0.632     0    0.653   0.621     2.635   82.143   84.422
LGA    G    12_A      G    12_A     2.119     0    0.113   0.113     2.119   75.238   75.238
LGA    H    13_A      H    13_A     2.165     0    0.656   1.490     5.366   57.857   49.810
LGA    D    14_A      D    14_A     0.834     0    0.000   1.238     4.883   65.595   59.702
LGA    E    15_A      E    15_A     6.996     0    0.663   0.813    12.858   16.905    7.884
LGA    Q    16_A      Q    16_A     8.545     0    0.674   1.092    13.957    2.619    1.640
LGA    E    17_A      E    17_A    12.066     0    0.044   1.002    15.837    0.000    0.000
LGA    L    18_A      L    18_A    19.201     0    0.097   1.358    23.471    0.000    0.000
LGA    P    19_A      P    19_A    24.623     0    0.000   0.104    27.400    0.000    0.000
LGA    F    20_A      F    20_A    30.434     0    0.037   1.441    32.540    0.000    0.000
LGA    K    21_A      K    21_A    37.186     0    0.000   0.220    39.642    0.000    0.000
LGA    K    22_A      K    22_A    40.270     0    0.000   0.462    49.137    0.000    0.000
LGA    G    23_A      G    23_A    42.289     0    0.000   0.000    42.289    0.000    0.000
LGA    E    24_A      E    24_A    38.612     0    0.052   0.968    39.425    0.000    0.000
LGA    I    25_A      I    25_A    36.347     0    0.052   0.619    41.146    0.000    0.000
LGA    L    26_A      L    26_A    29.977     0    0.000   0.942    31.948    0.000    0.000
LGA    R    27_A      R    27_A    28.227     0    0.022   0.078    32.406    0.000    0.000
LGA    I    28_A      I    28_A    21.185     0    0.052   0.050    23.926    0.000    0.000
LGA    R    29_A      R    29_A    20.942     0    0.634   1.069    27.827    0.000    0.000
LGA    D    30_A      D    30_A    16.963     0    0.664   1.084    20.769    0.000    0.000
LGA    K    31_A      K    31_A    14.948     0    0.308   0.347    21.916    0.000    0.000
LGA    P    32_A      P    32_A    13.664     0    0.129   0.384    16.058    0.000    0.000
LGA    E    33_A      E    33_A    10.716     0    0.698   1.065    13.173    0.476    0.212
LGA    E    34_A      E    34_A     6.839     0    0.189   1.013     8.580   19.048   12.963
LGA    Q    35_A      Q    35_A     0.800     0    0.429   0.472     5.329   72.024   60.423
LGA    L    36_A      L    36_A     0.585     0    0.365   0.744     3.291   78.095   81.071
LGA    W    37_A      W    37_A     0.442     0    0.041   0.291     1.487   97.619   90.612
LGA    N    38_A      N    38_A     0.505     0    0.000   0.932     2.914   95.238   85.357
LGA    A    39_A      A    39_A     0.070     0    0.022   0.062     0.443  100.000  100.000
LGA    E    40_A      E    40_A     0.036     0    0.012   0.224     1.259  100.000   95.820
LGA    N    41_A      N    41_A     0.038     0    0.000   0.341     1.636  100.000   96.607
LGA    V    42_A      V    42_A     0.277     0    0.041   1.121     2.837  100.000   87.755
LGA    E    43_A      E    43_A     0.193     0    0.051   0.319     1.139  100.000   96.878
LGA    G    44_A      G    44_A     0.239     0    0.000   0.000     0.320  100.000  100.000
LGA    K    45_A      K    45_A     0.269     0    0.020   0.957     4.946  100.000   78.254
LGA    R    46_A      R    46_A     0.135     0    0.068   0.100     0.308  100.000  100.000
LGA    G    47_A      G    47_A     0.194     0    0.000   0.000     0.219  100.000  100.000
LGA    L    48_A      L    48_A     0.302     0    0.000   1.106     2.978  100.000   90.238
LGA    I    49_A      I    49_A     0.415     0    0.039   0.096     0.506  100.000   98.810
LGA    H    50_A      H    50_A     0.457     0    0.000   0.220     1.807  100.000   88.048
LGA    V    51_A      V    51_A     0.395     0    0.000   0.055     0.516  100.000   98.639
LGA    V    52_A      V    52_A     0.287     0    0.049   0.102     0.745  100.000   97.279
LGA    L    53_A      L    53_A     0.309     0    0.000   1.038     2.684  100.000   90.060
LGA    V    54_A      V    54_A     0.305     0    0.040   0.089     0.436  100.000  100.000
LGA    E    55_A      E    55_A     0.153     0    0.000   0.356     1.755  100.000   90.847
LGA    K    56_A      K    56_A     0.357     0    0.053   0.952     4.127   95.238   76.931
LGA    Y    57_A      Y    57_A     0.654     0    0.571   0.477     3.110   86.071   71.468
LGA    G    58_A      G    58_A     4.001     0    0.362   0.362     5.463   34.881   34.881

# 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):    12.993         12.924                 13.356           59.368   55.214

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.93    65.086    57.453     3.604

LGA_LOCAL      RMSD:   0.927  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.144  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  12.993  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.486004 * X  +   0.842959 * Y  +   0.230696 * Z  + 204.587585
  Y_new =   0.826806 * X  +   0.357944 * Y  +   0.433899 * Z  + -359.242798
  Z_new =   0.283183 * X  +   0.401618 * Y  +  -0.870925 * Z  + -155.965836 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.102204 -0.287111  2.709514   [DEG:  120.4474  -16.4502  155.2437 ]
ZXZ:  2.652922  2.627878  0.614144   [DEG:  152.0012  150.5663   35.1878 ]
 
# END of job
