
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        2.61     2.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    44      18_B - 61_B        1.77     2.86
  LCS_AVERAGE:     60.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      20_B - 61_B        0.57     3.11
  LCS_AVERAGE:     55.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     17   18   61      8   16   17   22   28   46   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     17   18   61     13   16   17   22   31   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     17   18   61     13   16   16   22   28   37   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     17   18   61     13   16   17   22   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     17   18   61     13   16   17   41   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     17   18   61     13   16   16   22   35   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     17   18   61     13   16   17   22   43   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     17   18   61     13   16   20   41   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     17   18   61     13   16   17   31   43   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     17   18   61     13   16   17   22   34   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     17   18   61     13   16   18   33   43   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     17   18   61     13   16   17   29   43   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     17   18   61     10   16   17   22   31   44   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     17   18   61     13   16   17   22   31   43   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     17   18   61     13   16   17   22   31   44   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     17   18   61     11   16   16   19   28   30   34   53   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     17   18   61      4    5    8   15   17   26   27   31   33   46   55   60   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B      6   44   61      4    5    6    6    6   13   23   33   36   48   55   60   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B      6   44   61      4    5    6    6    6    7   45   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     42   44   61      4   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     42   44   61      9   41   42   42   45   50   54   58   59   59   59   59   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     42   44   61     17   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     42   44   61     23   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     42   44   61     22   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     42   44   61     23   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     42   44   61     11   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     42   44   61     21   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     42   44   61     11   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     42   44   61     24   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     42   44   61     27   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     42   44   61     10   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     42   44   61     23   41   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     42   44   61      3   39   42   42   45   50   54   58   59   59   59   60   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  71.92  (  55.50   60.25  100.00 )

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     27     41     42     42     45     50     54     58     59     59     59     60     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  44.26  67.21  68.85  68.85  73.77  81.97  88.52  95.08  96.72  96.72  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.53   0.57   0.57   0.99   1.50   1.85   2.10   2.19   2.19   2.19   2.59   2.61   2.61   2.61   2.61   2.61   2.61   2.61   2.61
GDT RMS_ALL_AT   3.19   3.13   3.11   3.11   2.99   2.81   2.70   2.65   2.64   2.64   2.64   2.61   2.61   2.61   2.61   2.61   2.61   2.61   2.61   2.61

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    53_B      E    53_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     3.303     0    0.510   1.250     5.291   47.619   59.643
LGA    Y     2_B      Y     2_B     2.882     0    0.095   1.380     7.792   55.357   45.040
LGA    I     3_B      I     3_B     3.647     0    0.043   0.056     5.477   48.333   40.655
LGA    R     4_B      R     4_B     2.417     0    0.045   0.480     5.340   64.881   52.424
LGA    E     5_B      E     5_B     1.814     0    0.025   0.720     2.194   68.810   74.974
LGA    L     6_B      L     6_B     3.135     0    0.029   0.420     5.675   51.786   42.560
LGA    R     7_B      R     7_B     2.806     0    0.021   0.350     6.662   59.048   41.472
LGA    A     8_B      A     8_B     1.945     0    0.045   0.052     2.382   66.786   68.000
LGA    A     9_B      A     9_B     2.881     0    0.017   0.022     3.535   51.905   52.952
LGA    L    10_B      L    10_B     3.725     0    0.016   0.071     4.692   46.667   41.964
LGA    I    11_B      I    11_B     2.903     0    0.029   0.042     3.379   51.786   58.274
LGA    L    12_B      L    12_B     3.232     0    0.078   0.147     3.977   46.667   48.333
LGA    L    13_B      L    13_B     4.131     0    0.054   0.568     4.887   37.262   36.488
LGA    A    14_B      A    14_B     4.648     0    0.055   0.053     5.025   31.548   32.667
LGA    L    15_B      L    15_B     4.385     0    0.065   0.274     5.543   31.786   38.512
LGA    K    16_B      K    16_B     5.386     0    0.551   0.962     5.807   29.048   34.656
LGA    K    17_B      K    17_B     8.504     0    0.126   0.760    17.898    7.619    3.386
LGA    Q    18_B      Q    18_B     8.547     0    0.100   1.325    15.380    8.571    3.810
LGA    H    19_B      H    19_B     4.504     0    0.035   0.373    11.664   39.286   19.571
LGA    A    20_B      A    20_B     2.628     0    0.665   0.599     4.647   65.476   58.667
LGA    E    21_B      E    21_B     2.808     0    0.160   0.484     4.722   62.976   48.783
LGA    D    22_B      D    22_B     2.263     0    0.031   0.266     2.804   68.810   62.976
LGA    P    23_B      P    23_B     1.036     0    0.085   0.326     1.530   81.429   81.497
LGA    D    24_B      D    24_B     1.296     0    0.058   0.209     1.771   81.429   80.357
LGA    A    25_B      A    25_B     1.547     0    0.027   0.031     1.634   79.286   78.000
LGA    Q    26_B      Q    26_B     1.346     0    0.066   0.289     2.166   81.429   77.672
LGA    R    27_B      R    27_B     1.012     0    0.015   0.268     1.174   83.690   88.009
LGA    V    28_B      V    28_B     1.220     0    0.024   0.042     1.267   81.429   81.429
LGA    A    29_B      A    29_B     1.414     0    0.016   0.020     1.448   81.429   81.429
LGA    D    30_B      D    30_B     1.250     0    0.041   0.649     1.332   81.429   82.560
LGA    E    31_B      E    31_B     1.022     0    0.015   0.191     1.243   81.429   85.450
LGA    L    32_B      L    32_B     1.072     0    0.030   0.057     1.268   81.429   82.560
LGA    M    33_B      M    33_B     1.360     0    0.041   0.825     2.380   81.429   75.119
LGA    K    34_B      K    34_B     1.223     0    0.057   0.859     6.263   81.429   60.635
LGA    K    35_B      K    35_B     0.901     0    0.021   0.246     1.037   85.952   90.582
LGA    L    36_B      L    36_B     1.195     0    0.019   1.283     4.003   81.429   67.202
LGA    F    37_B      F    37_B     1.595     0    0.023   0.370     3.200   75.000   67.229
LGA    D    38_B      D    38_B     1.502     0    0.012   0.224     2.244   77.143   76.131
LGA    A    39_B      A    39_B     1.144     0    0.018   0.028     1.361   81.429   83.238
LGA    A    40_B      A    40_B     1.417     0    0.084   0.096     1.980   77.143   78.000
LGA    H    41_B      H    41_B     1.885     0    0.081   0.911     3.712   70.833   61.476
LGA    R    42_B      R    42_B     1.920     0    0.022   0.838     4.000   72.857   66.061
LGA    N    43_B      N    43_B     1.747     0    0.073   0.255     2.003   77.143   73.988
LGA    D    44_B      D    44_B     1.397     0    0.063   0.185     1.671   81.548   80.417
LGA    K    45_B      K    45_B     1.283     0    0.016   0.283     2.982   83.690   75.185
LGA    D    46_B      D    46_B     0.875     0    0.026   0.125     1.403   88.214   84.821
LGA    K    47_B      K    47_B     0.616     0    0.021   0.639     4.711   90.476   72.116
LGA    V    48_B      V    48_B     0.872     0    0.016   0.036     1.297   90.476   86.599
LGA    K    49_B      K    49_B     0.582     0    0.065   0.431     3.356   92.857   82.116
LGA    K    50_B      K    50_B     0.556     0    0.021   0.359     1.826   92.857   90.635
LGA    V    51_B      V    51_B     0.738     0    0.023   0.037     1.151   90.476   89.184
LGA    V    52_B      V    52_B     0.539     0    0.030   0.066     0.683   90.476   90.476
LGA    E    53_B      E    53_B     0.554     0    0.023   0.411     1.482   92.857   89.524
LGA    E    54_B      E    54_B     0.803     0    0.047   0.951     3.485   90.476   78.307
LGA    A    55_B      A    55_B     0.719     0    0.015   0.021     0.820   90.476   90.476
LGA    K    56_B      K    56_B     0.555     0    0.032   0.380     1.393   90.476   91.587
LGA    K    57_B      K    57_B     0.632     0    0.018   0.066     1.523   90.476   86.508
LGA    V    58_B      V    58_B     0.989     0    0.153   0.236     2.055   88.214   82.925
LGA    V    59_B      V    59_B     1.152     0    0.037   0.179     1.579   81.429   80.204
LGA    S    60_B      S    60_B     0.967     0    0.257   0.299     1.085   88.214   88.968
LGA    T    61_B      T    61_B     1.125     0    0.064   0.085     1.287   81.429   82.721

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     2.609          2.524                  3.398           70.710   67.331

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     58    2.10    82.787    78.732     2.639

LGA_LOCAL      RMSD:   2.097  Number of atoms:   58  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.654  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.609  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.437485 * X  +  -0.549216 * Y  +   0.712017 * Z  +  -1.100029
  Y_new =   0.664409 * X  +  -0.730989 * Y  +  -0.155616 * Z  + -10.863851
  Z_new =   0.605943 * X  +   0.404991 * Y  +   0.684701 * Z  +   0.418082 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.153095 -0.650951  0.534136   [DEG:  123.3632  -37.2967   30.6037 ]
ZXZ:  1.355624  0.816603  0.981619   [DEG:   77.6715   46.7879   56.2426 ]
 
# END of job
