
#######################################################
#                                                     #
#                        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:    19       6_A - 24_A        4.87    14.95
  LONGEST_CONTINUOUS_SEGMENT:    19       8_A - 26_A        4.85    14.50
  LCS_AVERAGE:     53.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      20_A - 28_A        1.82    17.72
  LONGEST_CONTINUOUS_SEGMENT:     9      24_A - 32_A        1.81    19.07
  LCS_AVERAGE:     23.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      25_A - 31_A        0.94    19.35
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.96    19.07
  LCS_AVERAGE:     15.43

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      5    7   10      4    4    5    5    6    7    8    8    9   10   11   12   13   14   15   16   17   17   19   19 
LCS_GDT     R     2_A     R     2_A      5    7   10      4    4    5    5    6    7    8    8    9    9   11   12   13   14   15   16   17   17   19   19 
LCS_GDT     Q     3_A     Q     3_A      5    7   10      4    4    5    5    6    7    8    9    9   10   11   12   15   15   15   16   17   17   19   19 
LCS_GDT     S     4_A     S     4_A      5    7   10      4    4    5    5    6    7    8    9    9   10   11   12   15   15   15   16   17   17   19   19 
LCS_GDT     S     5_A     S     5_A      5    7   14      3    4    5    5    5    7    8    9    9    9   10   12   15   16   17   18   20   20   20   21 
LCS_GDT     A     6_A     A     6_A      4    7   19      3    4    4    4    6    7    8   10   10   12   15   17   17   19   19   19   22   23   24   24 
LCS_GDT     T     7_A     T     7_A      4    7   19      3    4    5    5    6    7    8   10   11   13   15   17   17   19   19   19   22   23   24   24 
LCS_GDT     S     8_A     S     8_A      4    4   19      3    4    4    4    6    7    8   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     S     9_A     S     9_A      5    6   19      3    4    5    5    5    8   10   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     F    10_A     F    10_A      5    6   19      3    4    5    5    6    8   10   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    11_A     G    11_A      5    6   19      3    4    5    5    6    8   10   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    12_A     G    12_A      5    6   19      3    4    5    5    6    8   10   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     L    13_A     L    13_A      5    6   19      3    4    5    5    5    6    8   12   13   13   15   17   17   19   19   22   22   22   24   24 
LCS_GDT     G    14_A     G    14_A      3    8   19      3    3    4    6    9   10   11   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    15_A     G    15_A      3    8   19      3    3    4    7    9   10   11   12   13   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    16_A     G    16_A      4    8   19      3    4    5    7    9   10   11   11   13   13   15   16   17   19   19   22   22   23   24   24 
LCS_GDT     S    17_A     S    17_A      4    8   19      3    4    5    7    9   10   11   11   12   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     V    18_A     V    18_A      4    8   19      3    4    5    7    9   10   11   11   12   13   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     R    19_A     R    19_A      4    8   19      3    4    5    7    9   10   11   11   12   14   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     F    20_A     F    20_A      5    9   19      3    5    7    8    9   10   13   13   13   14   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    21_A     G    21_A      5    9   19      3    5    7    8    9   10   13   13   13   14   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     P    22_A     P    22_A      5    9   19      3    5    7    8    9   10   13   13   13   14   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     G    23_A     G    23_A      5    9   19      3    5    7    8    9   10   13   13   13   14   15   17   17   19   19   22   22   23   24   24 
LCS_GDT     V    24_A     V    24_A      5    9   19      3    5    7    8    9   10   13   13   13   14   15   16   17   19   19   22   22   23   24   24 
LCS_GDT     A    25_A     A    25_A      7    9   19      3    5    7    7    8   10   13   13   13   14   15   16   16   18   19   22   22   23   24   24 
LCS_GDT     F    26_A     F    26_A      7    9   19      3    6    7    8    9   10   13   13   13   14   15   16   16   18   19   22   22   23   24   24 
LCS_GDT     R    27_A     R    27_A      7    9   18      3    6    7    7    9   10   13   13   13   14   15   16   16   17   19   22   22   23   24   24 
LCS_GDT     A    28_A     A    28_A      7    9   18      3    6    7    7    9   10   13   13   13   14   15   16   16   17   19   22   22   23   24   24 
LCS_GDT     P    29_A     P    29_A      7    9   18      3    6    7    7    8   10   13   13   13   14   15   16   16   17   19   22   22   23   24   24 
LCS_GDT     S    30_A     S    30_A      7    9   18      3    6    7    8    9   10   13   13   13   14   15   16   16   17   17   18   20   23   23   24 
LCS_GDT     I    31_A     I    31_A      7    9   18      3    6    7    7    8   10   13   13   13   14   15   16   16   17   17   18   20   23   23   24 
LCS_GDT     H    32_A     H    32_A      7    9   18      3    4    6    8    8   10   13   13   13   14   15   16   16   17   17   18   20   23   23   24 
LCS_GDT     G    33_A     G    33_A      3    8   18      3    3    3    4    4    7    8    8    9   14   15   16   16   17   17   18   19   23   23   24 
LCS_AVERAGE  LCS_A:  30.70  (  15.43   23.51   53.17 )

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      7      8      9     10     13     13     13     14     15     17     17     19     19     22     22     23     24     24 
GDT PERCENT_AT  12.12  18.18  21.21  24.24  27.27  30.30  39.39  39.39  39.39  42.42  45.45  51.52  51.52  57.58  57.58  66.67  66.67  69.70  72.73  72.73
GDT RMS_LOCAL    0.31   0.62   0.94   1.28   1.79   1.80   2.37   2.37   2.37   2.75   3.17   4.56   4.40   4.87   4.87   5.85   5.99   6.31   6.36   6.36
GDT RMS_ALL_AT  23.98  19.23  19.35  17.25  15.72  17.36  17.84  17.84  17.84  17.67  17.06  15.51  14.87  14.95  14.95  13.84  13.50  13.37  13.53  13.53

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    37.520     0    0.014   0.269    39.096    0.000    0.000
LGA    R     2_A      R     2_A    33.678     0    0.083   1.022    43.995    0.000    0.000
LGA    Q     3_A      Q     3_A    27.252     0    0.089   0.592    29.642    0.000    0.000
LGA    S     4_A      S     4_A    24.642     0    0.069   0.683    25.990    0.000    0.000
LGA    S     5_A      S     5_A    22.561     0    0.548   0.573    23.317    0.000    0.000
LGA    A     6_A      A     6_A    18.775     0    0.243   0.276    20.852    0.000    0.000
LGA    T     7_A      T     7_A    23.494     0    0.131   1.042    25.726    0.000    0.000
LGA    S     8_A      S     8_A    23.986     0    0.398   0.360    25.525    0.000    0.000
LGA    S     9_A      S     9_A    22.538     0    0.553   0.480    23.338    0.000    0.000
LGA    F    10_A      F    10_A    21.604     0    0.590   1.319    23.860    0.000    0.000
LGA    G    11_A      G    11_A    28.197     0    0.214   0.214    28.197    0.000    0.000
LGA    G    12_A      G    12_A    29.041     0    0.109   0.109    29.061    0.000    0.000
LGA    L    13_A      L    13_A    24.039     0    0.135   0.184    25.861    0.000    0.000
LGA    G    14_A      G    14_A    21.490     0    0.531   0.531    22.197    0.000    0.000
LGA    G    15_A      G    15_A    18.001     0    0.358   0.358    19.179    0.000    0.000
LGA    G    16_A      G    16_A    15.219     0    0.564   0.564    15.713    0.000    0.000
LGA    S    17_A      S    17_A    12.311     0    0.085   0.589    14.249    0.000    0.000
LGA    V    18_A      V    18_A     9.467     0    0.091   1.092     9.966    4.167    3.605
LGA    R    19_A      R    19_A     7.528     0    0.160   1.648    12.603   17.381    6.450
LGA    F    20_A      F    20_A     0.694     0    0.673   1.222     3.322   75.952   71.126
LGA    G    21_A      G    21_A     0.400     0    0.040   0.040     1.683   88.452   88.452
LGA    P    22_A      P    22_A     1.950     0    0.616   0.617     5.303   59.881   70.476
LGA    G    23_A      G    23_A     2.468     0    0.615   0.615     2.468   68.810   68.810
LGA    V    24_A      V    24_A     1.757     0    0.149   0.140     3.818   63.095   58.571
LGA    A    25_A      A    25_A     3.183     0    0.155   0.208     5.033   61.190   54.190
LGA    F    26_A      F    26_A     1.575     0    0.050   0.131     4.242   63.095   62.554
LGA    R    27_A      R    27_A     3.065     0    0.033   1.066    11.198   69.762   32.814
LGA    A    28_A      A    28_A     2.553     0    0.020   0.039     4.851   73.452   65.048
LGA    P    29_A      P    29_A     2.998     0    0.032   0.357     6.025   64.881   47.075
LGA    S    30_A      S    30_A     1.339     0    0.111   0.653     4.984   67.619   57.540
LGA    I    31_A      I    31_A     3.616     0    0.582   0.659    10.176   63.452   36.548
LGA    H    32_A      H    32_A     2.614     0    0.057   1.425     9.151   48.214   28.048
LGA    G    33_A      G    33_A     6.362     0    0.538   0.538     7.457   19.405   19.405

# 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):    12.033         11.865                 13.471           27.540   23.355

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     13    2.37    37.121    33.269     0.527

LGA_LOCAL      RMSD:   2.367  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.838  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  12.033  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.518920 * X  +   0.403475 * Y  +   0.753611 * Z  +   6.233878
  Y_new =  -0.025745 * X  +   0.888576 * Y  +  -0.458007 * Z  +  -0.571723
  Z_new =  -0.854435 * X  +   0.218267 * Y  +   0.471487 * Z  +   2.634852 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.049572  1.024463  0.433556   [DEG:   -2.8403   58.6974   24.8410 ]
ZXZ:  1.024698  1.079820 -1.320693   [DEG:   58.7109   61.8691  -75.6702 ]
 
# END of job
