
#######################################################
#                                                     #
#                        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   46 (  358),  selected   46 , name one
# Molecule2: number of CA atoms  353 ( 2869),  selected   46 , 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:    26     337_A - 362_A       4.75    10.75
  LCS_AVERAGE:      6.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     337_A - 349_A       1.92    15.30
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12     338_A - 349_A       0.99    14.04
  LCS_AVERAGE:      2.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   46
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     L   337_A     L   337_A      3   13   26      0    3    3    3    4    5    7   13   16   17   20   23   25   27   29   32   33   34   35   37 
LCS_GDT     Y   338_A     Y   338_A     12   13   26      9   10   11   12   12   13   16   17   20   22   23   25   26   27   28   31   33   34   35   36 
LCS_GDT     P   339_A     P   339_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     E   340_A     E   340_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     L   341_A     L   341_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     K   342_A     K   342_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     E   343_A     E   343_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     A   344_A     A   344_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     L   345_A     L   345_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     Q   346_A     Q   346_A     12   13   26      9   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     L   347_A     L   347_A     12   13   26      4   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     P   348_A     P   348_A     12   13   26      4   10   11   12   12   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     I   349_A     I   349_A     12   13   26      4    7   10   12   12   12   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     T   350_A     T   350_A      9   10   26      4    7    9   10   10   10   10   12   15   20   22   25   26   27   28   32   33   34   35   37 
LCS_GDT     E   351_A     E   351_A      9   10   26      4    7    9   10   10   10   10   11   13   17   17   21   26   27   29   32   33   34   35   37 
LCS_GDT     M   352_A     M   352_A      9   10   26      3    7    9   10   10   10   12   15   17   21   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     C   353_A     C   353_A      9   10   26      3    7    9   10   10   10   12   18   20   22   23   25   26   27   28   32   33   34   35   37 
LCS_GDT     Q   354_A     Q   354_A      9   10   26      3    7    9   10   10   10   13   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     K   355_A     K   355_A      9   10   26      3    7    8   10   10   11   15   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     C   356_A     C   356_A      9   10   26      3    6    9   10   10   11   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     T   357_A     T   357_A      4   10   26      3    4    4    5    6   13   16   16   17   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     R   358_A     R   358_A      4    6   26      3    4    4    8   11   13   16   18   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     R   359_A     R   359_A      4    6   26      3    4    4    5    9   13   16   17   20   22   23   25   26   27   29   32   33   34   35   37 
LCS_GDT     E   360_A     E   360_A      4    6   26      3    4    4    5    6    7    8   12   14   17   20   23   25   27   29   32   33   34   35   37 
LCS_GDT     V   361_A     V   361_A      4    6   26      3    4    4    5    6    7    8   12   14   15   18   20   23   27   29   32   33   34   35   37 
LCS_GDT     Y   362_A     Y   362_A      4    6   26      3    4    4    5    5    7    8   12   14   15   19   21   25   27   29   32   33   34   35   37 
LCS_GDT     G   363_A     G   363_A      4    6   21      3    4    4    5    6    7    8   12   14   15   16   20   23   27   29   32   33   34   35   37 
LCS_GDT     G   364_A     G   364_A      3    6   21      3    3    3    5    6    7    8   12   14   15   16   19   22   24   27   30   33   34   35   37 
LCS_GDT     V   365_A     V   365_A      3    6   21      0    3    3    5    5    7    8   12   14   15   16   17   19   20   25   27   30   31   32   35 
LCS_GDT     S   366_A     S   366_A      3    4   21      0    3    3    4    5    7    8   12   14   15   16   18   20   24   25   28   30   32   35   37 
LCS_GDT     E   367_A     E   367_A      4    5   21      0    3    4    4    5    5    8   12   14   15   16   18   20   24   26   28   31   33   35   37 
LCS_GDT     E   368_A     E   368_A      4    5   21      3    3    4    4    5    5    5    6    7    8   15   16   16   19   21   23   24   30   31   32 
LCS_GDT     G   369_A     G   369_A      4    5   21      3    3    4    4    5    5    8   12   14   15   16   17   19   22   25   28   30   32   35   37 
LCS_GDT     Q   370_A     Q   370_A      4    9   21      3    3    5    7    8    9   12   14   15   17   17   19   23   27   29   32   33   34   35   37 
LCS_GDT     F   371_A     F   371_A      3    9   21      3    3    4    7    8    9   12   14   15   17   18   20   23   27   29   32   33   34   35   37 
LCS_GDT     G   372_A     G   372_A      3   11   21      3    3    4    7    8   10   12   14   15   17   17   17   18   20   25   28   31   34   35   37 
LCS_GDT     G   373_A     G   373_A     10   11   21      4    4    9   10   10   10   12   14   15   17   17   19   22   27   29   32   33   34   35   37 
LCS_GDT     V   374_A     V   374_A     10   11   21      4    6    9   10   10   10   12   14   15   17   18   20   23   27   29   32   33   34   35   37 
LCS_GDT     V   375_A     V   375_A     10   11   21      4    8    9   10   10   10   12   14   15   17   17   19   23   27   29   32   33   34   35   37 
LCS_GDT     L   376_A     L   376_A     10   11   17      4    8    9   10   10   10   12   14   16   19   22   25   26   27   28   32   33   34   35   37 
LCS_GDT     C   377_A     C   377_A     10   11   17      6    8    9   10   10   10   12   14   15   17   22   25   26   27   28   29   30   30   33   34 
LCS_GDT     K   378_A     K   378_A     10   11   17      6    8    9   10   10   10   12   14   15   17   17   21   25   26   28   29   30   30   31   32 
LCS_GDT     D   379_A     D   379_A     10   11   17      6    8    9   10   10   10   12   14   15   18   18   21   25   27   28   29   30   30   31   32 
LCS_GDT     S   380_A     S   380_A     10   11   17      6    8    9   10   10   10   14   18   20   22   23   25   26   27   28   29   30   30   32   33 
LCS_GDT     Q   381_A     Q   381_A     10   11   17      6    8    9   10   10   11   15   18   20   22   23   25   26   27   28   29   30   30   32   32 
LCS_GDT     E   382_A     E   382_A     10   11   17      6    8    9   10   10   10   13   18   19   22   23   25   26   27   28   29   30   30   31   32 
LCS_AVERAGE  LCS_A:   3.88  (   2.27    2.80    6.58 )

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      9     10     11     12     12     13     16     18     20     22     23     25     26     27     29     32     33     34     35     37 
GDT PERCENT_AT   2.55   2.83   3.12   3.40   3.40   3.68   4.53   5.10   5.67   6.23   6.52   7.08   7.37   7.65   8.22   9.07   9.35   9.63   9.92  10.48
GDT RMS_LOCAL    0.32   0.45   0.73   0.99   0.99   1.96   2.38   2.94   3.19   3.37   3.50   3.79   3.97   4.17   5.61   5.91   5.96   6.13   6.28   6.78
GDT RMS_ALL_AT  15.51  15.09  14.56  14.04  14.04  12.00  11.94  14.31  13.29  13.84  13.88  13.69  13.74  14.14  10.03   9.81   9.90   9.84   9.95   9.77

# Checking swapping
#   possible swapping detected:  E   340_A      E   340_A
#   possible swapping detected:  E   351_A      E   351_A
#   possible swapping detected:  Y   362_A      Y   362_A
#   possible swapping detected:  E   367_A      E   367_A
#   possible swapping detected:  F   371_A      F   371_A
#   possible swapping detected:  E   382_A      E   382_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L   337_A      L   337_A    11.392     0    0.602   0.622    17.023    0.714    0.357
LGA    Y   338_A      Y   338_A     5.713     0    0.627   1.324     7.546   28.810   24.167
LGA    P   339_A      P   339_A     1.503     0    0.074   0.096     2.371   82.024   75.782
LGA    E   340_A      E   340_A     3.232     0    0.040   1.257     6.684   52.381   38.201
LGA    L   341_A      L   341_A     5.076     0    0.045   0.172     9.129   34.405   20.774
LGA    K   342_A      K   342_A     3.634     0    0.104   0.643    10.303   56.071   30.423
LGA    E   343_A      E   343_A     1.433     0    0.021   0.716     7.277   79.405   48.254
LGA    A   344_A      A   344_A     3.837     0    0.054   0.051     5.660   50.119   44.381
LGA    L   345_A      L   345_A     3.970     0    0.036   0.130     8.111   46.667   29.762
LGA    Q   346_A      Q   346_A     2.592     0    0.031   1.013     9.050   61.190   37.566
LGA    L   347_A      L   347_A     2.672     0    0.081   0.162     6.720   75.476   49.762
LGA    P   348_A      P   348_A     3.271     0    0.642   0.633     5.082   50.476   41.565
LGA    I   349_A      I   349_A     1.505     0    0.112   1.161     7.153   75.238   50.238
LGA    T   350_A      T   350_A     6.336     0    0.060   0.087     8.787   16.786   11.361
LGA    E   351_A      E   351_A     8.625     0    0.088   1.021    13.581    5.357    2.434
LGA    M   352_A      M   352_A     5.421     0    0.038   0.223     6.928   29.048   26.190
LGA    C   353_A      C   353_A     4.012     0    0.069   0.079     4.676   55.952   51.825
LGA    Q   354_A      Q   354_A     3.701     0    0.113   1.273     6.009   43.452   36.138
LGA    K   355_A      K   355_A     3.020     0    0.079   0.750     3.262   53.690   54.074
LGA    C   356_A      C   356_A     2.192     0    0.691   0.845     3.166   68.929   62.619
LGA    T   357_A      T   357_A     4.667     0    0.461   0.403     8.274   36.071   23.401
LGA    R   358_A      R   358_A     2.395     0    0.715   1.083    11.745   66.786   29.394
LGA    R   359_A      R   359_A     5.559     0    0.030   1.525     9.593   19.643   11.905
LGA    E   360_A      E   360_A    10.213     0    0.556   0.907    16.680    1.190    0.529
LGA    V   361_A      V   361_A    14.386     0    0.095   1.090    17.043    0.000    0.000
LGA    Y   362_A      Y   362_A    14.145     0    0.697   1.198    18.132    0.000    2.976
LGA    G   363_A      G   363_A    19.686     0    0.045   0.045    21.153    0.000    0.000
LGA    G   364_A      G   364_A    25.592     0    0.293   0.293    26.272    0.000    0.000
LGA    V   365_A      V   365_A    28.719     0    0.650   0.890    32.339    0.000    0.000
LGA    S   366_A      S   366_A    29.590     0    0.628   0.621    31.855    0.000    0.000
LGA    E   367_A      E   367_A    28.664     0    0.563   1.385    30.835    0.000    0.000
LGA    E   368_A      E   368_A    28.854     0    0.652   1.503    29.356    0.000    0.000
LGA    G   369_A      G   369_A    29.083     0    0.281   0.281    29.083    0.000    0.000
LGA    Q   370_A      Q   370_A    28.240     0    0.654   1.121    29.860    0.000    0.000
LGA    F   371_A      F   371_A    24.362     0    0.706   1.022    25.124    0.000    0.000
LGA    G   372_A      G   372_A    26.161     0    0.042   0.042    26.161    0.000    0.000
LGA    G   373_A      G   373_A    20.951     0    0.625   0.625    22.483    0.000    0.000
LGA    V   374_A      V   374_A    14.634     0    0.150   1.095    16.680    0.000    0.000
LGA    V   375_A      V   375_A    12.794     0    0.074   0.251    17.173    0.119    0.068
LGA    L   376_A      L   376_A     6.600     0    0.078   0.242     8.902    7.262   11.786
LGA    C   377_A      C   377_A     7.087     0    0.032   0.098     7.087   17.738   17.063
LGA    K   378_A      K   378_A     8.731     0    0.048   0.996    14.699    8.214    3.651
LGA    D   379_A      D   379_A     7.765     0    0.065   0.262    13.577   13.214    6.786
LGA    S   380_A      S   380_A     2.755     0    0.260   0.745     4.097   58.214   61.746
LGA    Q   381_A      Q   381_A     2.268     0    0.088   0.995    10.033   75.119   41.481
LGA    E   382_A      E   382_A     2.828     0    0.584   0.675     9.631   49.881   27.090

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       46     184    184  100.00     358    358  100.00               353
SUMMARY(RMSD_GDC):     9.180          9.070                 10.127            3.738    2.758

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   46  353    4.0     18    2.94     5.099     4.442     0.592

LGA_LOCAL      RMSD:   2.939  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.308  Number of assigned atoms:   46 
Std_ASGN_ATOMS RMSD:   9.180  Standard rmsd on all 46 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.633816 * X  +   0.698370 * Y  +   0.332501 * Z  + -54.770588
  Y_new =   0.317898 * X  +  -0.627088 * Y  +   0.711127 * Z  + -38.647476
  Z_new =   0.705138 * X  +  -0.345022 * Y  +  -0.619468 * Z  +  50.246506 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.464896 -0.782617 -2.633417   [DEG:   26.6366  -44.8407 -150.8837 ]
ZXZ:  2.704225  2.238861  2.025846   [DEG:  154.9407  128.2773  116.0724 ]
 
# END of job
