
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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      13_A - 33_A        4.67    10.89
  LCS_AVERAGE:     59.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      10_A - 20_A        2.00    15.84
  LCS_AVERAGE:     25.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      28_A - 33_A        0.98    16.91
  LCS_AVERAGE:     12.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      0    3   14      0    0    3    3    3    4    5    5    6   13   13   14   15   19   19   20   21   21   22   24 
LCS_GDT     R     2_A     R     2_A      3    4   14      0    1    3    3    4    4    5    9    9   13   13   16   18   19   19   20   21   21   22   24 
LCS_GDT     Q     3_A     Q     3_A      3    5   14      0    1    3    5    7    8    9   10   11   13   15   16   18   19   19   20   21   21   22   24 
LCS_GDT     S     4_A     S     4_A      3    5   15      0    1    3    5    7    8    9   10   11   13   15   16   18   19   19   20   21   21   22   24 
LCS_GDT     S     5_A     S     5_A      3    5   15      3    3    3    5    6    7    7    9   10   11   15   16   18   19   19   20   21   21   22   24 
LCS_GDT     A     6_A     A     6_A      3    5   20      3    3    3    4    6    7    7    9   11   14   15   16   18   19   19   20   21   21   22   24 
LCS_GDT     T     7_A     T     7_A      3    5   20      3    3    3    5    6    7   10   11   14   15   17   17   18   18   19   19   21   21   22   24 
LCS_GDT     S     8_A     S     8_A      3    4   20      3    3    3    4    5   10   12   14   15   15   17   17   18   18   19   19   20   21   22   24 
LCS_GDT     S     9_A     S     9_A      4   10   20      3    6    8   10   11   12   14   14   15   15   17   17   18   18   19   19   21   22   23   24 
LCS_GDT     F    10_A     F    10_A      4   11   20      3    6    8   10   11   12   14   14   15   15   17   17   18   18   19   19   21   22   23   24 
LCS_GDT     G    11_A     G    11_A      4   11   20      3    6    8   10   11   12   14   14   15   15   17   17   18   18   19   19   21   22   23   24 
LCS_GDT     G    12_A     G    12_A      4   11   20      3    5    8   10   11   12   14   14   15   15   17   17   18   18   19   19   21   22   23   24 
LCS_GDT     L    13_A     L    13_A      4   11   21      3    6    7   10   11   12   14   14   15   15   17   18   19   20   20   20   21   22   23   24 
LCS_GDT     G    14_A     G    14_A      4   11   21      3    5    8   10   11   12   14   14   15   15   17   18   19   20   20   20   21   22   23   24 
LCS_GDT     G    15_A     G    15_A      3   11   21      3    3    4   10   11   12   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     G    16_A     G    16_A      4   11   21      3    4    5    7   10   11   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     S    17_A     S    17_A      4   11   21      3    6    8   10   11   12   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     V    18_A     V    18_A      4   11   21      3    5    8   10   11   12   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     R    19_A     R    19_A      4   11   21      3    4    5    7   11   12   14   14   15   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     F    20_A     F    20_A      4   11   21      3    5    8   10   11   12   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     G    21_A     G    21_A      4    7   21      3    3    5    7    8   10   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     P    22_A     P    22_A      4    7   21      3    3    5    7   10   12   14   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     G    23_A     G    23_A      4    8   21      3    6    7    9   10   11   12   14   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     V    24_A     V    24_A      5    8   21      3    6    6    7    8   10   12   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     A    25_A     A    25_A      5    9   21      3    6    6    6    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     F    26_A     F    26_A      5    9   21      3    6    6    6    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     R    27_A     R    27_A      5    9   21      3    6    6    7    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     A    28_A     A    28_A      6    9   21      4    5    6    7    7    9   10   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     P    29_A     P    29_A      6    9   21      4    4    6    7    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     S    30_A     S    30_A      6    9   21      4    6    6    7    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     I    31_A     I    31_A      6    9   21      4    5    6    7    7    8   10   13   15   17   18   19   19   19   20   20   21   21   22   24 
LCS_GDT     H    32_A     H    32_A      6    9   21      4    6    6    7    7    9   11   13   16   18   18   19   19   20   20   20   21   22   23   24 
LCS_GDT     G    33_A     G    33_A      6    9   21      4    4    6    7    7    8   10   13   15   18   18   19   19   20   20   20   21   22   23   24 
LCS_AVERAGE  LCS_A:  32.66  (  12.49   25.53   59.96 )

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      4      6      8     10     11     12     14     14     16     18     18     19     19     20     20     20     21     22     23     24 
GDT PERCENT_AT  12.12  18.18  24.24  30.30  33.33  36.36  42.42  42.42  48.48  54.55  54.55  57.58  57.58  60.61  60.61  60.61  63.64  66.67  69.70  72.73
GDT RMS_LOCAL    0.34   0.55   1.00   1.36   1.62   1.78   2.26   2.26   3.36   3.65   3.65   3.81   3.81   4.45   4.25   4.25   4.67   5.74   6.31   6.44
GDT RMS_ALL_AT  15.59  10.43  15.75  15.82  16.27  16.41  16.01  16.01  11.45  11.43  11.43  11.59  11.59  10.76  11.23  11.23  10.89  10.12   9.77   9.73

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    23.801     0    0.254   1.412    26.768    0.000    0.000
LGA    R     2_A      R     2_A    21.336     0    0.444   1.136    25.436    0.000    0.000
LGA    Q     3_A      Q     3_A    22.458     0    0.611   1.458    26.686    0.000    0.000
LGA    S     4_A      S     4_A    20.341     0    0.437   0.686    23.223    0.000    0.000
LGA    S     5_A      S     5_A    20.183     0    0.580   0.692    20.840    0.000    0.000
LGA    A     6_A      A     6_A    14.431     0    0.117   0.145    16.059    0.000    0.000
LGA    T     7_A      T     7_A    11.003     0    0.459   0.445    13.935    2.857    1.633
LGA    S     8_A      S     8_A     7.752     0    0.591   0.530    11.506   15.000   10.238
LGA    S     9_A      S     9_A     2.259     0    0.645   0.560     4.213   50.952   51.825
LGA    F    10_A      F    10_A     1.991     0    0.241   1.253     9.219   68.929   39.004
LGA    G    11_A      G    11_A     1.194     0    0.725   0.725     2.570   79.881   79.881
LGA    G    12_A      G    12_A     1.028     0    0.311   0.311     4.421   66.190   66.190
LGA    L    13_A      L    13_A     2.577     0    0.250   0.308     8.619   71.310   42.500
LGA    G    14_A      G    14_A     1.251     0    0.386   0.386     3.513   67.619   67.619
LGA    G    15_A      G    15_A     3.072     0    0.153   0.153     3.072   65.238   65.238
LGA    G    16_A      G    16_A     3.816     0    0.230   0.230     5.230   44.167   44.167
LGA    S    17_A      S    17_A     1.081     0    0.170   0.198     1.949   79.286   77.143
LGA    V    18_A      V    18_A     0.497     0    0.190   1.182     3.868   82.262   73.265
LGA    R    19_A      R    19_A     2.559     0    0.173   1.147    10.920   71.310   33.333
LGA    F    20_A      F    20_A     1.685     0    0.625   1.139     9.597   81.786   40.216
LGA    G    21_A      G    21_A     3.443     0    0.130   0.130     3.443   61.071   61.071
LGA    P    22_A      P    22_A     2.295     0    0.456   1.013     4.979   59.167   49.796
LGA    G    23_A      G    23_A     6.228     0    0.418   0.418     6.979   22.738   22.738
LGA    V    24_A      V    24_A     8.923     0    0.040   0.053    12.889    1.429    3.333
LGA    A    25_A      A    25_A    13.610     0    0.486   0.455    15.100    0.000    0.000
LGA    F    26_A      F    26_A    13.898     0    0.112   0.894    17.644    0.000    0.000
LGA    R    27_A      R    27_A    18.182     0    0.625   1.049    19.767    0.000    0.000
LGA    A    28_A      A    28_A    20.441     0    0.101   0.135    23.357    0.000    0.000
LGA    P    29_A      P    29_A    21.921     0    0.201   0.401    25.394    0.000    0.000
LGA    S    30_A      S    30_A    28.105     0    0.131   0.661    31.410    0.000    0.000
LGA    I    31_A      I    31_A    31.131     0    0.052   0.077    34.398    0.000    0.000
LGA    H    32_A      H    32_A    34.060     0    0.609   0.944    37.596    0.000    0.000
LGA    G    33_A      G    33_A    31.733     0    0.451   0.451    32.968    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):     9.024          9.019                  9.846           30.036   25.127

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.26    37.879    37.217     0.593

LGA_LOCAL      RMSD:   2.263  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.012  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.024  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.408707 * X  +   0.908009 * Y  +  -0.092079 * Z  +  16.005219
  Y_new =  -0.631735 * X  +  -0.354272 * Y  +  -0.689494 * Z  +   6.518455
  Z_new =  -0.658688 * X  +  -0.223632 * Y  +   0.718415 * Z  +  10.677384 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.145031  0.719073 -0.301777   [DEG: -122.9012   41.1999  -17.2906 ]
ZXZ: -0.132760  0.769276 -1.898096   [DEG:   -7.6066   44.0763 -108.7529 ]
 
# END of job
