
#######################################################
#                                                     #
#                        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        4.49    14.70
  LCS_AVERAGE:     43.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.48    15.01
  LCS_AVERAGE:     32.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      35_A - 57_A        0.91    15.00
  LCS_AVERAGE:     26.13

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    4   10   12   31   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E     2_A     E     2_A     10   14   17      7   23   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     Y     3_A     Y     3_A     10   14   17      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     V     4_A     V     4_A     10   14   17      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     R     5_A     R     5_A     10   14   17      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     A     6_A     A     6_A     10   14   17      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     L     7_A     L     7_A     10   14   17     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     F     8_A     F     8_A     10   14   17     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     D     9_A     D     9_A     10   14   17     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     H    10_A     H    10_A     10   14   17      4   10   15   32   35   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     T    11_A     T    11_A     10   14   17     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     G    12_A     G    12_A      3   14   21      3    3   19   25   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     H    13_A     H    13_A      4   14   25      3    4   28   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     D    14_A     D    14_A      4   14   25      3   23   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    15_A     E    15_A      4   16   25      3    4    4    7   13   17   23   35   38   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     Q    16_A     Q    16_A     14   16   25      6    9   13   14   14   17   23   26   32   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    17_A     E    17_A     14   16   25      6   11   13   14   14   15   15   16   18   21   22   30   32   38   42   44   44   46   46   46 
LCS_GDT     L    18_A     L    18_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   26   31   37   39 
LCS_GDT     P    19_A     P    19_A     14   16   25      7   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     F    20_A     F    20_A     14   16   25      5    7   12   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     K    21_A     K    21_A     14   16   25      4   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     K    22_A     K    22_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     G    23_A     G    23_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     E    24_A     E    24_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     I    25_A     I    25_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     L    26_A     L    26_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     R    27_A     R    27_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   24   25   25   27   29 
LCS_GDT     I    28_A     I    28_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   26   29   30   35   36 
LCS_GDT     R    29_A     R    29_A     14   16   25      9   11   13   14   14   15   15   16   18   21   22   22   22   23   24   28   32   33   42   44 
LCS_GDT     D    30_A     D    30_A     10   16   29      3    4    8   10   14   15   15   16   18   21   22   22   28   30   35   41   45   46   46   46 
LCS_GDT     K    31_A     K    31_A      3    6   29      3    3    4    6    9   10   12   16   18   21   22   25   34   40   42   44   45   46   46   46 
LCS_GDT     P    32_A     P    32_A      3    6   29      3    3    4    4    5    8   11   13   18   21   22   22   26   29   43   44   45   46   46   46 
LCS_GDT     E    33_A     E    33_A      3    5   29      3    4    4    5    7    7   13   26   31   38   40   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    34_A     E    34_A      3   25   29      3    3   12   13   20   30   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     Q    35_A     Q    35_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     L    36_A     L    36_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     W    37_A     W    37_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     N    38_A     N    38_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     A    39_A     A    39_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    40_A     E    40_A     23   25   29     10   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     N    41_A     N    41_A     23   25   29     10   24   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     V    42_A     V    42_A     23   25   29     10   20   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    43_A     E    43_A     23   25   29     10   20   29   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     G    44_A     G    44_A     23   25   29     10   24   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     K    45_A     K    45_A     23   25   29     10   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     R    46_A     R    46_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     G    47_A     G    47_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     L    48_A     L    48_A     23   25   29     11   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     I    49_A     I    49_A     23   25   29     11   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     H    50_A     H    50_A     23   25   29     12   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     V    51_A     V    51_A     23   25   29      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     V    52_A     V    52_A     23   25   29      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     L    53_A     L    53_A     23   25   29      7   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     V    54_A     V    54_A     23   25   29     11   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     E    55_A     E    55_A     23   25   29     11   25   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     K    56_A     K    56_A     23   25   29      3   23   30   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     Y    57_A     Y    57_A     23   25   29      3   17   29   34   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_GDT     G    58_A     G    58_A     14   25   29      3    3   23   31   36   37   37   38   39   40   41   42   42   42   43   44   45   46   46   46 
LCS_AVERAGE  LCS_A:  34.16  (  26.13   32.52   43.82 )

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     12     25     30     34     36     37     37     38     39     40     41     42     42     42     43     44     45     46     46     46 
GDT PERCENT_AT  20.69  43.10  51.72  58.62  62.07  63.79  63.79  65.52  67.24  68.97  70.69  72.41  72.41  72.41  74.14  75.86  77.59  79.31  79.31  79.31
GDT RMS_LOCAL    0.35   0.67   0.87   1.04   1.21   1.27   1.27   1.48   1.72   2.10   2.41   2.76   2.76   2.76   3.23   3.67   4.13   4.36   4.36   4.36
GDT RMS_ALL_AT  14.92  15.00  14.97  14.98  15.01  15.01  15.01  15.00  14.96  14.86  14.76  14.72  14.72  14.72  14.67  14.58  14.46  14.37  14.37  14.37

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_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:  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    40_A      E    40_A
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     4.562     0    0.353   0.377     6.955   36.310   35.333
LGA    E     2_A      E     2_A     1.598     0    0.648   0.606     6.050   75.119   52.063
LGA    Y     3_A      Y     3_A     0.571     0    0.056   1.397     7.443   92.857   63.929
LGA    V     4_A      V     4_A     0.460     0    0.067   0.054     0.879   92.857   91.837
LGA    R     5_A      R     5_A     0.755     0    0.067   1.093     4.559   90.476   76.623
LGA    A     6_A      A     6_A     0.837     0    0.032   0.017     0.983   90.476   90.476
LGA    L     7_A      L     7_A     1.045     0    0.124   0.165     1.842   88.214   83.750
LGA    F     8_A      F     8_A     1.076     0    0.000   0.134     1.310   81.429   81.429
LGA    D     9_A      D     9_A     1.040     0    0.074   0.207     2.041   77.381   82.798
LGA    H    10_A      H    10_A     2.658     0    0.000   0.555     6.129   64.881   40.476
LGA    T    11_A      T    11_A     0.433     0    0.043   0.980     3.229   90.595   82.245
LGA    G    12_A      G    12_A     2.769     0    0.225   0.225     2.769   68.929   68.929
LGA    H    13_A      H    13_A     1.647     0    0.570   0.568     4.539   65.476   52.571
LGA    D    14_A      D    14_A     1.606     0    0.096   1.339     5.675   55.476   52.143
LGA    E    15_A      E    15_A     8.108     0    0.663   0.653    14.972   10.119    4.550
LGA    Q    16_A      Q    16_A     8.850     0    0.598   1.226    11.418    2.024    1.481
LGA    E    17_A      E    17_A    11.143     0    0.177   1.006    14.988    0.119    0.423
LGA    L    18_A      L    18_A    18.563     0    0.130   1.384    23.107    0.000    0.000
LGA    P    19_A      P    19_A    23.669     0    0.000   0.375    26.412    0.000    0.000
LGA    F    20_A      F    20_A    29.147     0    0.152   1.214    31.741    0.000    0.000
LGA    K    21_A      K    21_A    36.307     0    0.105   1.131    42.466    0.000    0.000
LGA    K    22_A      K    22_A    40.084     0    0.000   0.510    49.797    0.000    0.000
LGA    G    23_A      G    23_A    42.425     0    0.000   0.000    42.508    0.000    0.000
LGA    E    24_A      E    24_A    38.617     0    0.077   1.037    39.447    0.000    0.000
LGA    I    25_A      I    25_A    36.211     0    0.079   0.091    42.475    0.000    0.000
LGA    L    26_A      L    26_A    29.824     0    0.000   0.827    31.858    0.000    0.000
LGA    R    27_A      R    27_A    28.193     0    0.000   1.514    35.419    0.000    0.000
LGA    I    28_A      I    28_A    21.261     0    0.000   0.056    23.941    0.000    0.000
LGA    R    29_A      R    29_A    20.988     0    0.621   0.940    30.904    0.000    0.000
LGA    D    30_A      D    30_A    16.870     0    0.662   1.082    20.037    0.000    0.000
LGA    K    31_A      K    31_A    14.843     0    0.228   0.252    20.759    0.000    0.000
LGA    P    32_A      P    32_A    13.631     0    0.160   0.166    17.044    0.000    0.000
LGA    E    33_A      E    33_A    10.344     0    0.697   1.240    14.249    0.833    0.370
LGA    E    34_A      E    34_A     6.001     0    0.091   0.518     9.342   26.310   17.460
LGA    Q    35_A      Q    35_A     0.904     0    0.588   0.660     5.597   84.048   64.392
LGA    L    36_A      L    36_A     0.696     0    0.145   0.646     2.821   92.857   83.155
LGA    W    37_A      W    37_A     0.582     0    0.000   0.282     2.721   88.214   79.932
LGA    N    38_A      N    38_A     0.633     0    0.049   0.840     3.010   90.476   80.238
LGA    A    39_A      A    39_A     0.708     0    0.000   0.000     1.304   88.214   86.857
LGA    E    40_A      E    40_A     0.318     0    0.053   0.924     1.831   95.238   88.624
LGA    N    41_A      N    41_A     1.085     0    0.042   0.085     1.472   83.690   83.690
LGA    V    42_A      V    42_A     1.544     0    0.159   1.098     3.997   71.071   67.687
LGA    E    43_A      E    43_A     1.847     0    0.110   0.089     3.647   77.143   64.550
LGA    G    44_A      G    44_A     1.233     0    0.151   0.151     1.414   88.333   88.333
LGA    K    45_A      K    45_A     0.619     0    0.049   0.714     2.813   95.238   83.069
LGA    R    46_A      R    46_A     0.265     0    0.000   1.004     4.092   97.619   81.645
LGA    G    47_A      G    47_A     0.954     0    0.095   0.095     1.239   85.952   85.952
LGA    L    48_A      L    48_A     1.241     0    0.023   0.870     3.115   85.952   75.536
LGA    I    49_A      I    49_A     0.962     0    0.058   0.524     1.546   88.214   86.012
LGA    H    50_A      H    50_A     0.818     0    0.087   0.996     5.446   88.214   63.095
LGA    V    51_A      V    51_A     0.738     0    0.037   0.056     1.289   88.214   87.891
LGA    V    52_A      V    52_A     0.804     0    0.221   1.073     3.448   88.214   78.435
LGA    L    53_A      L    53_A     0.918     0    0.075   0.123     1.412   88.214   84.821
LGA    V    54_A      V    54_A     0.553     0    0.000   0.040     0.660   90.476   90.476
LGA    E    55_A      E    55_A     1.053     0    0.131   0.865     2.298   88.214   81.640
LGA    K    56_A      K    56_A     1.414     0    0.026   0.909     2.049   79.286   77.831
LGA    Y    57_A      Y    57_A     1.985     0    0.571   1.332     6.389   63.452   49.563
LGA    G    58_A      G    58_A     3.014     0    0.537   0.537     4.935   43.690   43.690

# 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):    12.916         12.827                 13.306           54.140   48.897

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.48    60.776    55.340     2.411

LGA_LOCAL      RMSD:   1.476  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.996  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  12.916  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.402341 * X  +   0.888556 * Y  +   0.220430 * Z  + 167.879074
  Y_new =   0.912463 * X  +   0.369652 * Y  +   0.175408 * Z  + -398.257568
  Z_new =   0.074377 * X  +   0.271708 * Y  +  -0.959501 * Z  + -61.476185 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.986090 -0.074446  2.865641   [DEG:  113.7946   -4.2654  164.1891 ]
ZXZ:  2.242942  2.856023  0.267194   [DEG:  128.5111  163.6381   15.3091 ]
 
# END of job
