
#######################################################
#                                                     #
#                        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 (  457),  selected   58 , name one
# Molecule2: number of CA atoms  192 ( 1575),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    55       3_D - 57_D        4.80     5.53
  LCS_AVERAGE:     28.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      27_D - 45_D        1.79     6.53
  LCS_AVERAGE:      8.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      31_D - 45_D        0.89     7.44
  LCS_AVERAGE:      5.74

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     S     3_D     S     3_D      7   15   55      3    3    6    9   16   21   27   34   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I     4_D     I     4_D     12   15   55      3    8   11   16   20   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     T     5_D     T     5_D     12   15   55      7    8   11   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     H     6_D     H     6_D     12   15   55      7   10   11   16   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     A     7_D     A     7_D     12   15   55      7   10   11   15   22   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E     8_D     E     8_D     12   15   55      7   10   11   16   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     F     9_D     F     9_D     12   15   55      7   10   11   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    10_D     E    10_D     12   15   55      7   10   11   15   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     F    11_D     F    11_D     12   15   55      7   10   11   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     S    12_D     S    12_D     12   15   55      3   10   11   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     L    13_D     L    13_D     12   15   55      5   10   11   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     L    14_D     L    14_D     12   15   55      5   10   12   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    15_D     E    15_D     12   15   55      5   10   11   16   21   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     N    16_D     N    16_D      8   15   55      5    7    9   15   20   26   30   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     V    17_D     V    17_D      8   15   55      5    7    9   16   21   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     K    18_D     K    18_D      3   11   55      3    3    7    9   12   14   22   26   29   34   37   42   47   50   50   53   54   55   55   55 
LCS_GDT     Y    19_D     Y    19_D      3   11   55      3    5    9   16   20   26   30   35   35   37   41   46   49   50   51   54   54   55   55   55 
LCS_GDT     E    20_D     E    20_D      6   10   55      3    5    7   10   15   20   31   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     T    21_D     T    21_D      6   10   55      3    5    7   10   12   14   20   28   31   36   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    22_D     E    22_D      6   10   55      3    5    7   10   12   15   22   28   31   36   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     D    23_D     D    23_D      6   10   55      3    5    7   10   12   15   22   28   31   36   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    24_D     E    24_D      6   10   55      3    5    7   10   12   16   25   32   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     V    25_D     V    25_D      6   10   55      3    5    7   13   20   24   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     P    26_D     P    26_D      4   10   55      3    4    4    8   10   10   18   22   25   34   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I    27_D     I    27_D      6   19   55      3    5    9   14   19   23   28   34   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     V    28_D     V    28_D      6   19   55      5    5   10   16   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     L    29_D     L    29_D      6   19   55      5   10   13   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    30_D     E    30_D      6   19   55      5    5    7   11   20   25   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     Y    31_D     Y    31_D     15   19   55      7   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     K    32_D     K    32_D     15   19   55      6   13   14   16   21   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    33_D     E    33_D     15   19   55      6   13   14   16   19   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     E    34_D     E    34_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I    35_D     I    35_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I    36_D     I    36_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     N    37_D     N    37_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     L    38_D     L    38_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I    39_D     I    39_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     K    40_D     K    40_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     K    41_D     K    41_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     F    42_D     F    42_D     15   19   55     10   13   14   17   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     S    43_D     S    43_D     15   19   55     10   13   14   16   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     N    44_D     N    44_D     15   19   55      4   12   14   16   20   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     S    45_D     S    45_D     15   19   55      4   12   13   16   23   26   32   35   37   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     G    46_D     G    46_D      4   16   55      4    4    8   14   15   16   18   20   28   31   38   46   49   50   52   54   54   55   55   55 
LCS_GDT     Q    47_D     Q    47_D      4   15   55      4    4    5    9   14   16   18   21   26   34   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     S    48_D     S    48_D     13   15   55      3   13   13   14   15   16   18   20   25   33   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     G    49_D     G    49_D     13   15   55      3   13   13   14   15   16   22   27   31   34   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     M    50_D     M    50_D     13   15   55      3   13   13   14   15   16   18   20   22   26   31   45   49   50   52   54   54   55   55   55 
LCS_GDT     S    51_D     S    51_D     13   15   55      4   13   13   14   15   16   18   20   21   25   31   36   40   49   52   54   54   55   55   55 
LCS_GDT     A    52_D     A    52_D     13   15   55      4   13   13   14   15   16   23   28   34   37   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     P    53_D     P    53_D     13   15   55      4   13   13   14   15   21   25   30   35   38   41   46   49   50   52   54   54   55   55   55 
LCS_GDT     I    54_D     I    54_D     13   15   55      4   13   13   14   15   16   18   20   24   30   35   41   48   49   52   54   54   55   55   55 
LCS_GDT     T    55_D     T    55_D     13   15   55      4   13   13   14   15   16   18   20   23   30   35   38   45   49   52   54   54   55   55   55 
LCS_GDT     A    56_D     A    56_D     13   15   55      4   13   13   14   15   16   18   20   28   34   39   42   48   49   52   54   54   55   55   55 
LCS_GDT     S    57_D     S    57_D     13   15   55      4   13   13   14   15   16   18   20   23   30   35   38   45   49   52   54   54   55   55   55 
LCS_GDT     I    58_D     I    58_D     13   15   34      4   13   13   14   15   16   18   20   21   22   25   28   34   35   39   43   44   51   53   55 
LCS_GDT     I    59_D     I    59_D     13   15   30      4   13   13   14   15   16   18   20   21   21   23   26   28   30   36   37   44   45   50   54 
LCS_GDT     T    60_D     T    60_D     13   15   30      4   13   13   14   15   16   17   20   21   22   23   27   29   35   38   43   44   51   53   55 
LCS_AVERAGE  LCS_A:  13.95  (   5.74    8.12   28.01 )

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     10     13     14     17     23     26     32     35     37     38     41     46     49     50     52     54     54     55     55     55 
GDT PERCENT_AT   5.21   6.77   7.29   8.85  11.98  13.54  16.67  18.23  19.27  19.79  21.35  23.96  25.52  26.04  27.08  28.13  28.13  28.65  28.65  28.65
GDT RMS_LOCAL    0.34   0.55   0.72   1.56   1.81   1.95   2.33   2.53   2.78   2.92   3.27   3.93   4.16   4.26   4.49   4.69   4.67   4.80   4.80   4.80
GDT RMS_ALL_AT   7.18   8.03   7.87   6.74   6.39   6.41   6.40   6.64   6.26   6.03   5.84   5.61   5.66   5.72   5.53   5.50   5.57   5.53   5.53   5.53

# Checking swapping
#   possible swapping detected:  F     9_D      F     9_D
#   possible swapping detected:  F    11_D      F    11_D
#   possible swapping detected:  Y    19_D      Y    19_D
#   possible swapping detected:  E    22_D      E    22_D
#   possible swapping detected:  Y    31_D      Y    31_D
#   possible swapping detected:  E    33_D      E    33_D
#   possible swapping detected:  E    34_D      E    34_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     3_D      S     3_D     5.498     0    0.261   0.520     7.233   27.500   22.222
LGA    I     4_D      I     4_D     3.251     0    0.258   0.326     5.437   55.714   44.464
LGA    T     5_D      T     5_D     1.935     0    0.041   0.064     4.126   70.833   61.088
LGA    H     6_D      H     6_D     2.778     0    0.016   1.160     7.688   62.976   40.857
LGA    A     7_D      A     7_D     2.519     0    0.021   0.023     3.215   66.905   63.524
LGA    E     8_D      E     8_D     1.563     0    0.027   0.493     5.787   75.000   52.698
LGA    F     9_D      F     9_D     2.893     0    0.054   0.071     7.468   57.262   34.069
LGA    E    10_D      E    10_D     3.304     0    0.059   0.585     5.666   53.571   42.116
LGA    F    11_D      F    11_D     1.816     0    0.011   0.508     3.966   70.833   63.810
LGA    S    12_D      S    12_D     2.224     0    0.023   0.683     4.263   64.881   58.968
LGA    L    13_D      L    13_D     2.981     0    0.036   1.208     7.020   60.952   48.929
LGA    L    14_D      L    14_D     1.461     0    0.033   1.380     3.634   77.143   72.381
LGA    E    15_D      E    15_D     2.194     0    0.069   0.437     4.171   59.524   57.672
LGA    N    16_D      N    16_D     3.599     0    0.018   1.072     7.138   48.452   40.238
LGA    V    17_D      V    17_D     2.792     0    0.607   1.271     6.310   40.714   46.803
LGA    K    18_D      K    18_D     7.247     0    0.625   1.319    17.697   15.833    7.196
LGA    Y    19_D      Y    19_D     4.140     0    0.568   1.419    11.396   34.524   22.302
LGA    E    20_D      E    20_D     3.636     0    0.287   1.497     7.960   35.476   25.820
LGA    T    21_D      T    21_D     7.280     0    0.152   0.216     9.029   15.833   10.068
LGA    E    22_D      E    22_D     8.263     0    0.235   1.370    10.062    4.286    2.963
LGA    D    23_D      D    23_D     9.364     0    0.096   0.412    13.483    1.905    0.952
LGA    E    24_D      E    24_D     6.797     0    0.100   0.798     7.288   15.357   13.175
LGA    V    25_D      V    25_D     4.040     0    0.669   0.580     6.092   27.976   35.510
LGA    P    26_D      P    26_D     8.310     0    0.568   0.629     9.919   11.310    8.027
LGA    I    27_D      I    27_D     6.013     0    0.024   0.223     9.471   30.357   20.298
LGA    V    28_D      V    28_D     2.928     0    0.120   1.251     4.697   66.548   53.129
LGA    L    29_D      L    29_D     1.793     0    0.047   1.111     5.224   63.214   54.524
LGA    E    30_D      E    30_D     3.542     0    0.119   0.186     5.807   48.452   37.354
LGA    Y    31_D      Y    31_D     1.207     0    0.431   0.421     1.577   81.548   83.730
LGA    K    32_D      K    32_D     2.902     0    0.066   0.920     9.004   57.143   38.307
LGA    E    33_D      E    33_D     3.167     0    0.020   0.178     5.738   57.381   41.429
LGA    E    34_D      E    34_D     1.870     0    0.041   1.293     3.635   72.976   66.296
LGA    I    35_D      I    35_D     0.826     0    0.047   0.660     3.622   90.476   79.107
LGA    I    36_D      I    36_D     1.204     0    0.021   0.764     3.132   81.429   76.667
LGA    N    37_D      N    37_D     0.909     0    0.048   0.120     2.143   92.976   82.976
LGA    L    38_D      L    38_D     0.770     0    0.065   1.391     4.830   88.333   70.298
LGA    I    39_D      I    39_D     1.432     0    0.024   0.870     2.596   79.286   75.179
LGA    K    40_D      K    40_D     0.764     0    0.082   0.791     3.630   90.476   75.026
LGA    K    41_D      K    41_D     1.009     0    0.104   1.068     6.870   79.524   55.767
LGA    F    42_D      F    42_D     1.838     0    0.015   0.520     2.714   69.048   75.411
LGA    S    43_D      S    43_D     2.381     0    0.097   0.620     4.156   59.524   55.397
LGA    N    44_D      N    44_D     2.998     0    0.042   0.603     3.787   53.571   53.690
LGA    S    45_D      S    45_D     3.109     0    0.058   0.633     5.725   38.690   41.349
LGA    G    46_D      G    46_D     9.477     0    0.138   0.138    12.588    3.690    3.690
LGA    Q    47_D      Q    47_D    10.877     0    0.584   1.384    12.367    0.000    0.000
LGA    S    48_D      S    48_D    10.724     0    0.106   0.105    10.897    0.000    0.079
LGA    G    49_D      G    49_D    11.614     0    0.409   0.409    12.176    0.000    0.000
LGA    M    50_D      M    50_D    14.026     0    0.053   0.687    17.527    0.000    0.000
LGA    S    51_D      S    51_D    12.879     0    0.119   0.240    13.411    0.000    0.000
LGA    A    52_D      A    52_D     8.368     0    0.110   0.124     9.933    5.595    6.476
LGA    P    53_D      P    53_D     8.316     0    0.133   0.170     9.660    2.976    2.177
LGA    I    54_D      I    54_D    12.101     0    0.072   0.219    16.422    0.000    0.000
LGA    T    55_D      T    55_D    10.920     0    0.085   0.100    11.887    0.119    0.068
LGA    A    56_D      A    56_D     7.494     0    0.027   0.057     8.716    5.595    7.905
LGA    S    57_D      S    57_D    10.361     0    0.132   0.561    12.403    0.357    0.238
LGA    I    58_D      I    58_D    14.139     0    0.085   0.230    16.421    0.000    0.000
LGA    I    59_D      I    59_D    12.949     0    0.197   1.341    14.298    0.000    0.060
LGA    T    60_D      T    60_D    11.625     0    0.597   0.546    13.036    0.000    0.680

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     457    457  100.00               192
SUMMARY(RMSD_GDC):     5.465          5.509                  6.056           12.365   10.589

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58  192    4.0     35    2.53    15.495    14.043     1.330

LGA_LOCAL      RMSD:   2.531  Number of atoms:   35  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.642  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:   5.465  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.874400 * X  +  -0.444011 * Y  +  -0.195651 * Z  + -20.433655
  Y_new =   0.453561 * X  +   0.604735 * Y  +   0.654658 * Z  +  -0.112245
  Z_new =  -0.172359 * X  +  -0.661173 * Y  +   0.730167 * Z  + -39.350807 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.478505  0.173224 -0.735850   [DEG:   27.4163    9.9250  -42.1611 ]
ZXZ: -2.851182  0.752230 -2.886582   [DEG: -163.3607   43.0996 -165.3890 ]
 
# END of job
