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

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.39    15.11
  LCS_AVERAGE:     32.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.57    15.12
  LCS_AVERAGE:     29.46

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   17   27   32   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     24   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   15   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    9   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     24   34   34   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    5    9   11   15   21   31   36   38   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      8   14   14   15   15   15   18   26   31   38   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     11   14   14   15   15   15   16   18   20   22   22   22   27   32   36   40   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   32   36   38 
LCS_GDT     P    19_A     P    19_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   24   25   28   30   34   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     12   14   14   15   15   15   16   18   20   22   22   22   22   23   26   30   33   34   36   38 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    6   11   15   15   15   16   18   20   22   22   22   27   32   33   35   43   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   16   18   20   22   24   24   27   39   42   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    7   29      3    3    4    6    7   12   16   18   21   26   29   33   38   39   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    7   29      3    3    4    5    7   10   12   26   32   38   39   40   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      3   25   29      3    3    4    4    6   13   33   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29     14   34   35   36   37   37   37   37   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     29   34   35   36   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      0    5   31   35   37   37   37   38   39   40   41   41   42   42   43   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.40  (  29.46   32.91   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     35     36     37     37     37     38     39     40     41     41     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  50.00  58.62  60.34  62.07  63.79  63.79  63.79  65.52  67.24  68.97  70.69  70.69  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.27   0.37   0.64   0.66   0.76   0.76   0.76   1.61   1.60   1.96   2.28   2.28   2.68   2.68   3.14   3.58   3.58   3.94   4.35   4.35
GDT RMS_ALL_AT  15.14  15.14  15.18  15.17  15.14  15.14  15.14  15.05  15.05  14.96  14.86  14.86  14.84  14.84  14.80  14.71  14.71  14.59  14.48  14.48

# Checking swapping
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_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:  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     5.797     0    0.403   0.442     7.605   30.476   27.048
LGA    E     2_A      E     2_A     0.970     0    0.662   1.051     7.729   86.071   49.365
LGA    Y     3_A      Y     3_A     0.727     0    0.039   0.170     1.237   90.476   87.460
LGA    V     4_A      V     4_A     0.643     0    0.031   1.186     2.902   90.476   82.041
LGA    R     5_A      R     5_A     0.527     0    0.016   1.114     4.643   95.238   77.576
LGA    A     6_A      A     6_A     0.134     0    0.032   0.046     0.216  100.000  100.000
LGA    L     7_A      L     7_A     0.268     0    0.100   0.179     0.992   97.619   94.048
LGA    F     8_A      F     8_A     0.429     0    0.055   0.148     1.724  100.000   88.268
LGA    D     9_A      D     9_A     0.479     0    0.039   0.205     1.575   97.619   93.036
LGA    H    10_A      H    10_A     0.461     0    0.067   0.255     0.978   95.238   95.238
LGA    T    11_A      T    11_A     0.707     0    0.611   1.045     2.998   82.143   78.435
LGA    G    12_A      G    12_A     1.602     0    0.094   0.094     1.602   79.405   79.405
LGA    H    13_A      H    13_A     2.031     0    0.516   1.526     4.363   57.857   56.429
LGA    D    14_A      D    14_A     1.793     0    0.073   1.078     5.506   53.214   53.988
LGA    E    15_A      E    15_A     7.685     0    0.627   1.551    13.341   11.310    5.185
LGA    Q    16_A      Q    16_A     8.479     0    0.638   1.325    14.051    3.095    1.746
LGA    E    17_A      E    17_A    12.350     0    0.077   1.163    15.895    0.000    0.000
LGA    L    18_A      L    18_A    19.334     0    0.097   1.396    23.477    0.000    0.000
LGA    P    19_A      P    19_A    24.821     0    0.038   0.213    27.507    0.000    0.000
LGA    F    20_A      F    20_A    30.677     0    0.033   1.435    32.794    0.000    0.000
LGA    K    21_A      K    21_A    37.443     0    0.053   0.212    39.911    0.000    0.000
LGA    K    22_A      K    22_A    40.385     0    0.024   0.703    46.989    0.000    0.000
LGA    G    23_A      G    23_A    42.281     0    0.049   0.049    42.281    0.000    0.000
LGA    E    24_A      E    24_A    38.534     0    0.034   1.105    39.364    0.000    0.000
LGA    I    25_A      I    25_A    36.145     0    0.055   0.103    42.438    0.000    0.000
LGA    L    26_A      L    26_A    29.772     0    0.012   0.052    31.792    0.000    0.000
LGA    R    27_A      R    27_A    27.802     0    0.032   1.301    31.001    0.000    0.000
LGA    I    28_A      I    28_A    20.653     0    0.048   0.104    23.430    0.000    0.000
LGA    R    29_A      R    29_A    20.298     0    0.599   1.174    29.254    0.000    0.000
LGA    D    30_A      D    30_A    16.117     0    0.697   0.904    20.613    0.000    0.000
LGA    K    31_A      K    31_A    13.978     0    0.214   0.303    20.448    0.000    0.000
LGA    P    32_A      P    32_A    12.828     0    0.064   0.083    16.331    0.000    0.000
LGA    E    33_A      E    33_A    10.058     0    0.720   0.833    12.380    2.381    1.058
LGA    E    34_A      E    34_A     5.645     0    0.275   0.973     6.868   28.333   23.598
LGA    Q    35_A      Q    35_A     1.303     0    0.650   1.652     6.961   83.690   50.847
LGA    L    36_A      L    36_A     1.190     0    0.070   1.040     3.407   81.429   73.393
LGA    W    37_A      W    37_A     0.974     0    0.022   0.247     2.383   88.214   81.701
LGA    N    38_A      N    38_A     0.590     0    0.046   0.571     1.987   90.476   88.274
LGA    A    39_A      A    39_A     0.429     0    0.033   0.037     0.429  100.000  100.000
LGA    E    40_A      E    40_A     0.541     0    0.013   0.486     1.587   92.857   88.571
LGA    N    41_A      N    41_A     0.637     0    0.032   0.201     1.411   88.214   87.083
LGA    V    42_A      V    42_A     1.277     0    0.061   1.141     3.527   81.429   75.986
LGA    E    43_A      E    43_A     0.844     0    0.201   0.894     3.662   83.810   73.704
LGA    G    44_A      G    44_A     0.889     0    0.054   0.054     0.915   90.476   90.476
LGA    K    45_A      K    45_A     0.795     0    0.064   0.819     5.710   90.476   68.254
LGA    R    46_A      R    46_A     0.401     0    0.040   0.259     2.087  100.000   85.974
LGA    G    47_A      G    47_A     0.114     0    0.021   0.021     0.382  100.000  100.000
LGA    L    48_A      L    48_A     0.522     0    0.029   0.149     0.668   92.857   91.667
LGA    I    49_A      I    49_A     0.743     0    0.017   0.076     0.904   90.476   90.476
LGA    H    50_A      H    50_A     1.255     0    0.017   1.192     4.274   81.429   69.905
LGA    V    51_A      V    51_A     1.248     0    0.035   0.094     1.398   83.690   82.721
LGA    V    52_A      V    52_A     1.178     0    0.110   1.091     3.598   88.333   80.000
LGA    L    53_A      L    53_A     0.642     0    0.103   1.041     3.252   92.857   84.345
LGA    V    54_A      V    54_A     0.402     0    0.033   0.109     0.648   97.619   97.279
LGA    E    55_A      E    55_A     0.713     0    0.021   0.820     3.746   90.476   71.746
LGA    K    56_A      K    56_A     0.836     0    0.068   0.841     4.771   90.476   74.497
LGA    Y    57_A      Y    57_A     0.738     0    0.575   0.554     2.654   84.048   81.111
LGA    G    58_A      G    58_A     2.033     0    0.286   0.286     4.079   52.500   52.500

# 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):    13.023         12.946                 13.389           57.186   52.318

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.61    65.517    57.561     2.226

LGA_LOCAL      RMSD:   1.607  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.054  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.023  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.662549 * X  +   0.538605 * Y  +  -0.520512 * Z  + -32.030827
  Y_new =   0.314034 * X  +  -0.830646 * Y  +  -0.459793 * Z  +  28.942699
  Z_new =  -0.680008 * X  +   0.141177 * Y  +  -0.719484 * Z  + -21.494305 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.442614  0.747774  2.947835   [DEG:   25.3599   42.8443  168.8985 ]
ZXZ: -0.847258  2.373856 -1.366094   [DEG:  -48.5443  136.0119  -78.2714 ]
 
# END of job
