
#######################################################
#                                                     #
#                        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:    25       3_A - 27_A        4.92    10.38
  LONGEST_CONTINUOUS_SEGMENT:    25       4_A - 28_A        4.97    10.34
  LCS_AVERAGE:     70.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       9_A - 21_A        1.92    12.40
  LCS_AVERAGE:     29.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.98    15.62
  LCS_AVERAGE:     14.69

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      4    4   12      0    3    4    4    4    4    4    4    4    5   13   19   20   20   20   20   21   23   24   25 
LCS_GDT     R     2_A     R     2_A      4    4   13      1    3    4    4    4   12   14   14   15   17   18   19   20   21   22   23   24   25   26   26 
LCS_GDT     Q     3_A     Q     3_A      4    4   25      0    3    4    4    4    4   14   14   15   17   18   19   20   21   22   23   24   25   26   26 
LCS_GDT     S     4_A     S     4_A      4    5   25      3    3    4    7   10   12   14   14   15   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     S     5_A     S     5_A      3    5   25      3    3    5    5    8   12   14   16   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     A     6_A     A     6_A      3    5   25      3    3    4    5    7    8   11   16   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     T     7_A     T     7_A      3    5   25      3    3    4    5    6    7   11   16   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     S     8_A     S     8_A      3    5   25      3    3    4    5    8   12   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     S     9_A     S     9_A      4   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     F    10_A     F    10_A      4   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    11_A     G    11_A      4   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    12_A     G    12_A      4   13   25      3    4    5    8   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     L    13_A     L    13_A      4   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    14_A     G    14_A      4   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    15_A     G    15_A      5   13   25      2    5    5    8   10   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    16_A     G    16_A      5   13   25      3    4    5   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     S    17_A     S    17_A      5   13   25      3    4    6   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     V    18_A     V    18_A      5   13   25      3    5    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     R    19_A     R    19_A      5   13   25      3    5    5   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     F    20_A     F    20_A      5   13   25      3    5    5   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    21_A     G    21_A      5   13   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     P    22_A     P    22_A      5    9   25      3    5    5    6    9   14   16   16   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     G    23_A     G    23_A      5    9   25      3    7    8   10   13   14   16   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     V    24_A     V    24_A      5   10   25      4    5    8    9   10   12   15   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     A    25_A     A    25_A      6   10   25      4    4    8    9   10   12   14   17   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     F    26_A     F    26_A      7   10   25      4    5    8    9   10   12   14   15   18   22   22   22   22   23   23   23   24   25   26   26 
LCS_GDT     R    27_A     R    27_A      7   10   25      4    5    8    9   10   12   14   14   15   17   18   19   20   23   23   23   23   25   26   26 
LCS_GDT     A    28_A     A    28_A      7   10   25      4    5    8    9   10   12   14   14   15   17   18   19   20   20   20   20   22   25   26   26 
LCS_GDT     P    29_A     P    29_A      7   10   21      4    5    8    9   10   12   14   14   15   17   18   19   20   20   20   22   23   25   26   26 
LCS_GDT     S    30_A     S    30_A      7   10   19      4    5    8    9   10   12   14   14   15   17   18   19   20   20   20   20   22   25   26   26 
LCS_GDT     I    31_A     I    31_A      7   10   19      3    5    8    9    9   11   14   14   15   17   18   19   20   20   20   20   21   23   23   24 
LCS_GDT     H    32_A     H    32_A      7   10   19      4    5    8    9   10   12   14   14   15   17   18   19   20   20   20   20   22   25   26   26 
LCS_GDT     G    33_A     G    33_A      3   10   19      0    3    6    8   10   12   14   14   15   17   18   19   20   20   20   20   21   23   23   25 
LCS_AVERAGE  LCS_A:  38.45  (  14.69   29.75   70.89 )

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      7      8     10     13     14     16     17     18     22     22     22     22     23     23     23     24     25     26     26 
GDT PERCENT_AT  12.12  21.21  24.24  30.30  39.39  42.42  48.48  51.52  54.55  66.67  66.67  66.67  66.67  69.70  69.70  69.70  72.73  75.76  78.79  78.79
GDT RMS_LOCAL    0.25   0.85   0.92   1.26   1.73   1.93   2.33   2.63   2.78   3.45   3.45   3.45   3.45   3.81   3.81   3.81   4.63   5.07   5.32   5.32
GDT RMS_ALL_AT  13.36  13.01  12.97  12.49  12.42  12.41  12.07  11.94  11.77  10.99  10.99  10.99  10.99  10.86  10.86  10.86  10.37  10.19  10.10  10.10

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    20.933     0    0.212   1.370    22.671    0.000    0.000
LGA    R     2_A      R     2_A    16.639     0    0.273   1.204    17.822    0.000    0.043
LGA    Q     3_A      Q     3_A    16.271     0    0.335   1.129    22.500    0.000    0.000
LGA    S     4_A      S     4_A    11.558     0    0.598   0.764    12.951    0.119    0.556
LGA    S     5_A      S     5_A     6.751     0    0.511   0.820     8.166   16.667   19.841
LGA    A     6_A      A     6_A     6.357     0    0.709   0.640     7.592   13.690   12.381
LGA    T     7_A      T     7_A     5.757     0    0.081   0.096     9.283   36.786   24.150
LGA    S     8_A      S     8_A     4.299     0    0.541   0.739     6.378   36.190   31.349
LGA    S     9_A      S     9_A     2.619     0    0.618   0.936     5.139   62.381   52.143
LGA    F    10_A      F    10_A     0.763     0    0.411   1.073     9.140   79.524   46.537
LGA    G    11_A      G    11_A     2.221     0    0.157   0.157     2.754   71.190   71.190
LGA    G    12_A      G    12_A     2.614     0    0.107   0.107     3.555   61.548   61.548
LGA    L    13_A      L    13_A     1.732     0    0.070   0.076     7.138   69.286   46.607
LGA    G    14_A      G    14_A     1.197     0    0.178   0.178     3.984   65.595   65.595
LGA    G    15_A      G    15_A     3.659     0    0.641   0.641     3.659   57.500   57.500
LGA    G    16_A      G    16_A     2.820     0    0.403   0.403     3.013   59.286   59.286
LGA    S    17_A      S    17_A     1.775     0    0.085   0.105     4.044   81.548   68.889
LGA    V    18_A      V    18_A     0.837     0    0.154   0.206     3.468   73.690   69.932
LGA    R    19_A      R    19_A     3.047     0    0.105   1.213     8.651   71.548   33.766
LGA    F    20_A      F    20_A     2.403     0    0.121   0.950    10.745   50.833   24.675
LGA    G    21_A      G    21_A     1.733     0    0.186   0.186     2.640   69.048   69.048
LGA    P    22_A      P    22_A     5.103     0    0.122   0.606     7.613   36.071   24.966
LGA    G    23_A      G    23_A     1.294     0    0.575   0.575     2.758   67.143   67.143
LGA    V    24_A      V    24_A     3.701     0    0.379   0.387     7.000   40.595   31.905
LGA    A    25_A      A    25_A     4.078     0    0.167   0.170     4.408   43.571   42.286
LGA    F    26_A      F    26_A     5.750     0    0.108   1.085    12.435   15.595    7.489
LGA    R    27_A      R    27_A     9.029     0    0.081   1.136    12.764    2.857    1.991
LGA    A    28_A      A    28_A    14.677     0    0.099   0.121    17.199    0.000    0.000
LGA    P    29_A      P    29_A    16.138     0    0.059   0.613    19.888    0.000    0.000
LGA    S    30_A      S    30_A    19.267     0    0.105   0.595    22.121    0.000    0.000
LGA    I    31_A      I    31_A    26.616     0    0.631   0.593    31.502    0.000    0.000
LGA    H    32_A      H    32_A    26.566     0    0.623   0.951    27.632    0.000    0.000
LGA    G    33_A      G    33_A    30.875     0    0.505   0.505    33.741    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):     8.087          8.109                  8.632           35.826   30.025

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     17    2.63    43.182    42.845     0.623

LGA_LOCAL      RMSD:   2.628  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.941  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   8.087  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.946937 * X  +  -0.113965 * Y  +   0.300535 * Z  +  12.005379
  Y_new =  -0.142861 * X  +  -0.688359 * Y  +  -0.711163 * Z  +  78.331520
  Z_new =   0.287924 * X  +  -0.716361 * Y  +   0.635552 * Z  +   3.838197 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.991856 -0.292058 -0.845101   [DEG: -171.4207  -16.7337  -48.4207 ]
ZXZ:  0.399833  0.882073  2.759427   [DEG:   22.9088   50.5391  158.1035 ]
 
# END of job
