
#######################################################
#                                                     #
#                        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   53 (  449),  selected   53 , name one
# Molecule2: number of CA atoms  222 ( 1756),  selected   53 , 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:    21      58_A - 78_A        4.95    21.76
  LCS_AVERAGE:      8.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      59_A - 70_A        1.74    17.24
  LCS_AVERAGE:      3.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      59_A - 68_A        0.80    17.36
  LCS_AVERAGE:      2.63

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   53
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     N    31_A     N    31_A      3    3   11      0    3    3    3    3    4    5    6    7    9   10   11   12   13   16   16   18   18   18   21 
LCS_GDT     K    32_A     K    32_A      3    4   12      1    3    3    3    3    4    6    8    9   10   10   11   14   14   16   17   18   18   18   18 
LCS_GDT     H    33_A     H    33_A      3    6   12      0    3    4    5    6    6    6    8    9   10   10   11   14   14   16   17   18   18   18   21 
LCS_GDT     I    34_A     I    34_A      4    6   15      1    4    4    5    6    6    6    8    9   10   10   11   14   15   16   17   18   20   20   21 
LCS_GDT     P    35_A     P    35_A      4    6   15      3    4    4    4    6    6    6    8    9   11   12   14   14   16   18   19   19   21   22   24 
LCS_GDT     F    36_A     F    36_A      4    6   15      3    4    4    5    6    6    6    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     Y    37_A     Y    37_A      4    6   15      3    4    4    5    6    6    7   16   16   16   16   20   20   21   22   22   24   25   27   27 
LCS_GDT     H    38_A     H    38_A      4    6   15      4    5    6    8   11   13   14   16   16   16   18   20   20   21   22   22   24   25   27   27 
LCS_GDT     I    39_A     I    39_A      4    5   15      4    5    6    8   11   13   14   16   16   16   18   20   20   21   22   22   24   25   27   27 
LCS_GDT     E    40_A     E    40_A      4    7   15      3    4    4    6    6    7    8    9   11   13   15   17   20   21   22   22   24   25   27   27 
LCS_GDT     D    41_A     D    41_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     S    42_A     S    42_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     K    43_A     K    43_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     F    44_A     F    44_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     K    45_A     K    45_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   20   21   24   25 
LCS_GDT     H    46_A     H    46_A      5    7   15      4    4    5    7    7    8    8    9   11   12   12   14   15   17   18   19   20   21   22   25 
LCS_GDT     Y    47_A     Y    47_A      5    7   15      4    4    5    7    7    8    8    9   11   12   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     G    48_A     G    48_A      4    6   15      3    3    4    4    6    8    8    9   10   11   13   14   15   17   18   19   21   23   27   27 
LCS_GDT     K    49_A     K    49_A      5    6   15      2    4    5    5    6    7    8    9   10   11   13   14   15   17   18   19   20   22   24   25 
LCS_GDT     V    50_A     V    50_A      5    5   16      3    4    5    5    6    6    8    9   10   11   12   13   15   17   18   19   20   21   23   25 
LCS_GDT     I    51_A     I    51_A      5    5   18      3    4    5    5    6    6    8    8   10   12   14   14   16   18   18   19   21   23   27   27 
LCS_GDT     N    52_A     N    52_A      5    5   18      3    4    5    5    6    6    8    8   11   11   14   14   17   18   18   19   21   23   27   27 
LCS_GDT     E    53_A     E    53_A      5    5   18      3    4    5    5    6    6    8    8   11   12   15   15   17   18   18   19   21   23   27   27 
LCS_GDT     Y    54_A     Y    54_A      3    5   18      3    3    4    4    6    6    8    9   13   13   15   15   17   18   18   20   21   23   27   27 
LCS_GDT     D    55_A     D    55_A      3    5   19      3    3    4    4    4    6   11   11   13   13   15   15   17   18   19   21   24   25   26   26 
LCS_GDT     F    56_A     F    56_A      3    5   20      3    3    4    4    5    9   11   11   13   15   18   20   20   21   22   22   24   25   27   27 
LCS_GDT     N    57_A     N    57_A      3    5   20      0    3    4    4    5    9   11   11   13   15   18   20   20   21   22   22   24   25   27   27 
LCS_GDT     E    58_A     E    58_A      3   11   21      0    3    4    4    6    8   11   11   14   16   18   20   20   21   22   22   24   25   26   27 
LCS_GDT     L    59_A     L    59_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   20   21   22   22   24   25   27   27 
LCS_GDT     E    60_A     E    60_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   20   21   22   23   24   25   27   27 
LCS_GDT     T    61_A     T    61_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     Y    62_A     Y    62_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     M    63_A     M    63_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     D    64_A     D    64_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     S    65_A     S    65_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     L    66_A     L    66_A     10   12   21      7    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     T    67_A     T    67_A     10   12   21      3    9   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     I    68_A     I    68_A     10   12   21      4    8   10   10   12   13   14   16   16   16   18   20   21   21   22   23   24   25   27   27 
LCS_GDT     P    69_A     P    69_A      5   12   21      4    5    5    6   12   13   14   16   16   16   18   20   21   21   22   23   24   25   26   26 
LCS_GDT     Q    70_A     Q    70_A      5   12   21      4    5    5    6    8   13   14   16   16   16   18   20   21   21   22   23   24   25   25   26 
LCS_GDT     D    71_A     D    71_A      5    8   21      4    5    5    6    7    9   14   14   14   14   14   17   19   21   22   23   24   25   25   26 
LCS_GDT     Q    72_A     Q    72_A      3    6   21      3    3    9    9   12   13   14   16   16   16   18   20   21   21   22   23   24   25   26   26 
LCS_GDT     N    73_A     N    73_A      8   10   21      3    4    6    8    9   10   10   11   12   14   17   20   21   21   22   23   24   25   26   26 
LCS_GDT     V    74_A     V    74_A      8   10   21      3    6    7    8    9   10   10   11   14   16   16   18   21   21   22   23   24   25   26   26 
LCS_GDT     Y    75_A     Y    75_A      8   10   21      4    6    7    8    9   10   10   11   13   16   16   18   21   21   22   23   24   25   26   26 
LCS_GDT     V    76_A     V    76_A      8   10   21      4    6    7    8    9   10   10   11   12   16   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     A    77_A     A    77_A      8   10   21      4    6    7    8    9   10   10   11   12   14   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     S    78_A     S    78_A      8   10   21      4    6    7    8    9   10   10   11   12   14   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     V    79_A     V    79_A      8   10   20      3    6    7    8    9   10   10   11   12   14   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     T    80_A     T    80_A      8   10   20      3    5    7    8    9   10   10   11   12   14   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     E    81_A     E    81_A      4   10   20      3    4    6    8    9   10   10   11   12   14   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     M    82_A     M    82_A      4   10   20      3    4    6    8    9   10   10   11   11   11   16   18   21   21   22   23   24   25   25   25 
LCS_GDT     E    83_A     E    83_A      3   10   20      3    3    5    5    5    9   10   11   11   11   14   17   18   18   18   22   24   24   25   25 
LCS_AVERAGE  LCS_A:   4.84  (   2.63    3.70    8.18 )

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      7      9     10     10     12     13     14     16     16     16     18     20     21     21     22     23     24     25     27     27 
GDT PERCENT_AT   3.15   4.05   4.50   4.50   5.41   5.86   6.31   7.21   7.21   7.21   8.11   9.01   9.46   9.46   9.91  10.36  10.81  11.26  12.16  12.16
GDT RMS_LOCAL    0.24   0.71   0.80   0.80   1.40   1.76   2.23   2.75   2.75   2.75   3.83   4.16   4.96   4.30   4.51   5.39   5.22   5.64   7.41   7.41
GDT RMS_ALL_AT  17.87  17.63  17.36  17.36  17.49  17.48  15.79  15.56  15.56  15.56  15.43  15.32  25.43  15.40  15.32  25.07  15.30  15.30  14.56  14.56

# Checking swapping
#   possible swapping detected:  F    36_A      F    36_A
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    62_A      Y    62_A
#   possible swapping detected:  Y    75_A      Y    75_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    31_A      N    31_A    27.673     0    0.505   0.777    28.562    0.000    0.000
LGA    K    32_A      K    32_A    27.322     0    0.691   0.576    30.971    0.000    0.000
LGA    H    33_A      H    33_A    25.293     0    0.645   1.032    26.241    0.000    0.000
LGA    I    34_A      I    34_A    19.229     0    0.166   0.668    21.204    0.000    0.000
LGA    P    35_A      P    35_A    16.050     0    0.199   0.251    19.919    0.000    0.000
LGA    F    36_A      F    36_A     8.940     0    0.182   0.354    11.609    3.214   24.242
LGA    Y    37_A      Y    37_A     4.080     0    0.567   1.535     7.205   46.548   29.087
LGA    H    38_A      H    38_A     3.085     0    0.231   0.813    11.264   63.095   28.714
LGA    I    39_A      I    39_A     2.981     0    0.131   0.606     6.852   46.905   39.881
LGA    E    40_A      E    40_A     8.039     0    0.690   1.090    11.870    5.476    3.122
LGA    D    41_A      D    41_A    12.821     0    0.286   0.742    16.549    0.000    0.000
LGA    S    42_A      S    42_A    16.245     0    0.057   0.102    17.979    0.000    0.000
LGA    K    43_A      K    43_A    17.643     0    0.133   1.259    18.388    0.000    0.000
LGA    F    44_A      F    44_A    16.557     0    0.146   0.131    17.779    0.000    0.000
LGA    K    45_A      K    45_A    17.893     2    0.094   0.695    19.459    0.000    0.000
LGA    H    46_A      H    46_A    18.556     0    0.049   0.868    19.302    0.000    0.000
LGA    Y    47_A      Y    47_A    18.333     0    0.525   1.452    25.188    0.000    0.000
LGA    G    48_A      G    48_A    19.309     0    0.124   0.124    21.223    0.000    0.000
LGA    K    49_A      K    49_A    22.870     4    0.481   0.534    23.180    0.000    0.000
LGA    V    50_A      V    50_A    20.365     0    0.639   1.340    21.810    0.000    0.000
LGA    I    51_A      I    51_A    19.376     0    0.073   1.197    19.814    0.000    0.000
LGA    N    52_A      N    52_A    18.916     0    0.728   0.622    20.424    0.000    0.000
LGA    E    53_A      E    53_A    18.612     0    0.667   1.319    18.711    0.000    0.000
LGA    Y    54_A      Y    54_A    16.965     0    0.587   0.420    21.237    0.000    0.000
LGA    D    55_A      D    55_A    15.006     0    0.627   0.873    20.855    0.000    0.000
LGA    F    56_A      F    56_A     9.704     0    0.640   1.211    11.819    0.595    9.394
LGA    N    57_A      N    57_A     9.450     0    0.647   1.197    13.346    1.548    0.833
LGA    E    58_A      E    58_A     8.302     0    0.632   0.831    16.029    9.167    4.074
LGA    L    59_A      L    59_A     2.903     0    0.615   0.525     4.940   55.595   50.655
LGA    E    60_A      E    60_A     2.038     0    0.027   1.097     7.114   73.095   45.873
LGA    T    61_A      T    61_A     0.735     0    0.030   1.179     3.728   85.952   77.347
LGA    Y    62_A      Y    62_A     2.205     0    0.044   0.395     5.103   70.833   50.238
LGA    M    63_A      M    63_A     1.977     0    0.055   0.242     5.301   77.143   58.333
LGA    D    64_A      D    64_A     1.277     0    0.100   0.279     3.174   81.548   70.357
LGA    S    65_A      S    65_A     1.687     0    0.159   0.230     2.384   79.286   74.444
LGA    L    66_A      L    66_A     0.839     0    0.068   0.083     3.215   81.548   72.440
LGA    T    67_A      T    67_A     3.217     0    0.529   1.301     4.271   50.476   46.531
LGA    I    68_A      I    68_A     3.196     0    0.139   0.163     9.859   55.714   35.714
LGA    P    69_A      P    69_A     2.807     0    0.106   0.135     5.726   66.905   50.340
LGA    Q    70_A      Q    70_A     3.337     0    0.635   1.005     9.093   39.643   24.392
LGA    D    71_A      D    71_A     6.222     3    0.594   0.554     8.968   26.548   13.631
LGA    Q    72_A      Q    72_A     4.344     3    0.142   0.673     6.407   28.214   19.577
LGA    N    73_A      N    73_A     8.467     0    0.556   1.142     9.881    5.000    5.119
LGA    V    74_A      V    74_A    11.399     0    0.033   1.055    12.604    0.000    0.000
LGA    Y    75_A      Y    75_A    15.509     0    0.063   1.345    23.942    0.000    0.000
LGA    V    76_A      V    76_A    18.671     0    0.055   0.125    20.440    0.000    0.000
LGA    A    77_A      A    77_A    23.302     0    0.108   0.110    25.045    0.000    0.000
LGA    S    78_A      S    78_A    25.235     0    0.081   0.546    26.688    0.000    0.000
LGA    V    79_A      V    79_A    23.598     0    0.631   0.990    24.265    0.000    0.000
LGA    T    80_A      T    80_A    26.247     0    0.599   0.855    28.820    0.000    0.000
LGA    E    81_A      E    81_A    21.216     0    0.196   1.637    23.109    0.000    0.000
LGA    M    82_A      M    82_A    19.116     0    0.067   0.868    20.221    0.000    0.000
LGA    E    83_A      E    83_A    23.521     0    0.036   0.783    28.047    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       53     212    212  100.00     437    437  100.00               222
SUMMARY(RMSD_GDC):    13.485         13.402                 13.779            4.748    3.758

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53  222    4.0     16    2.75     6.532     5.883     0.562

LGA_LOCAL      RMSD:   2.745  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.564  Number of assigned atoms:   53 
Std_ASGN_ATOMS RMSD:  13.485  Standard rmsd on all 53 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.651351 * X  +  -0.648438 * Y  +  -0.394042 * Z  + 150.605469
  Y_new =  -0.161211 * X  +   0.625720 * Y  +  -0.763207 * Z  + 193.998444
  Z_new =   0.741453 * X  +  -0.433592 * Y  +  -0.512099 * Z  + 141.480499 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.898965 -0.835233 -2.439021   [DEG: -166.0985  -47.8553 -139.7456 ]
ZXZ: -0.476601  2.108423  2.099954   [DEG:  -27.3072  120.8038  120.3185 ]
 
# END of job
