
#######################################################
#                                                     #
#                        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:    33       1_A - 33_A        2.83     2.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      16_A - 29_A        1.98     3.10
  LONGEST_CONTINUOUS_SEGMENT:    14      17_A - 30_A        1.98     3.10
  LCS_AVERAGE:     32.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      18_A - 24_A        0.97     6.34
  LCS_AVERAGE:     15.79

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      6    8   33      5    5    9   16   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R     2_A     R     2_A      6    8   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     Q     3_A     Q     3_A      6    8   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S     4_A     S     4_A      6    8   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S     5_A     S     5_A      6    8   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A     6_A     A     6_A      6    8   33      5    5    9   10   15   23   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     T     7_A     T     7_A      3    8   33      3    5   11   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S     8_A     S     8_A      3    8   33      3    3    4    5   11   23   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S     9_A     S     9_A      5    6   33      3    5   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     F    10_A     F    10_A      5    6   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    11_A     G    11_A      5    6   33      3    6   12   16   20   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    12_A     G    12_A      5    6   33      3    5    5    9   19   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L    13_A     L    13_A      5    6   33      3    5    5    7   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    14_A     G    14_A      3    6   33      3    5    9   12   19   23   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    15_A     G    15_A      3    6   33      3    5    5    5    5   11   13   18   26   30   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    16_A     G    16_A      3   14   33      3    5   10   16   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S    17_A     S    17_A      3   14   33      3    5   10   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    18_A     V    18_A      7   14   33      3    3    9   13   17   21   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R    19_A     R    19_A      7   14   33      3    5    9   13   18   22   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     F    20_A     F    20_A      7   14   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    21_A     G    21_A      7   14   33      4    6   12   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     P    22_A     P    22_A      7   14   33      4    8   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    23_A     G    23_A      7   14   33      4    6   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    24_A     V    24_A      7   14   33      4    6   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A    25_A     A    25_A      5   14   33      5    5    8   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     F    26_A     F    26_A      5   14   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R    27_A     R    27_A      5   14   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A    28_A     A    28_A      5   14   33      5    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     P    29_A     P    29_A      5   14   33      5    5   12   16   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S    30_A     S    30_A      5   14   33      4    9   14   18   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     I    31_A     I    31_A      5   13   33      4    5    5    8    9   20   25   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     H    32_A     H    32_A      5   13   33      3    5   14   17   21   24   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    33_A     G    33_A      4    9   33      3    4    5    6    9   21   26   30   32   32   33   33   33   33   33   33   33   33   33   33 
LCS_AVERAGE  LCS_A:  49.34  (  15.79   32.23  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      5      9     14     18     21     24     26     30     32     32     33     33     33     33     33     33     33     33     33     33 
GDT PERCENT_AT  15.15  27.27  42.42  54.55  63.64  72.73  78.79  90.91  96.97  96.97 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.14   0.68   1.01   1.38   1.56   1.81   2.00   2.42   2.60   2.60   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83
GDT RMS_ALL_AT   9.80   3.13   3.13   2.94   2.98   2.92   2.93   2.86   2.84   2.84   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83   2.83

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_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     2.708     0    0.200   1.070    13.415   69.048   29.960
LGA    R     2_A      R     2_A     1.539     0    0.135   0.837     3.389   75.119   71.775
LGA    Q     3_A      Q     3_A     1.119     0    0.046   1.039     4.714   81.429   71.481
LGA    S     4_A      S     4_A     1.368     0    0.033   0.655     3.410   88.333   79.365
LGA    S     5_A      S     5_A     1.076     0    0.583   0.835     2.786   73.214   73.175
LGA    A     6_A      A     6_A     4.015     0    0.091   0.146     6.867   52.262   44.476
LGA    T     7_A      T     7_A     1.949     0    0.579   1.384     4.614   75.119   64.830
LGA    S     8_A      S     8_A     3.586     0    0.624   0.808     7.358   55.833   42.460
LGA    S     9_A      S     9_A     1.880     0    0.671   0.759     6.299   81.548   63.413
LGA    F    10_A      F    10_A     1.045     0    0.131   0.449     3.056   79.286   70.216
LGA    G    11_A      G    11_A     3.273     0    0.085   0.085     3.273   57.262   57.262
LGA    G    12_A      G    12_A     3.417     0    0.555   0.555     3.417   59.405   59.405
LGA    L    13_A      L    13_A     2.258     0    0.631   0.535     5.157   64.881   51.429
LGA    G    14_A      G    14_A     4.278     0    0.618   0.618     4.955   39.286   39.286
LGA    G    15_A      G    15_A     6.985     0    0.037   0.037     6.985   24.762   24.762
LGA    G    16_A      G    16_A     2.693     0    0.479   0.479     4.730   58.571   58.571
LGA    S    17_A      S    17_A     2.068     0    0.265   0.651     6.253   54.524   45.397
LGA    V    18_A      V    18_A     4.552     0    0.643   0.539     7.001   44.643   30.748
LGA    R    19_A      R    19_A     3.918     0    0.037   1.605     5.074   52.619   47.489
LGA    F    20_A      F    20_A     1.249     0    0.578   0.691     4.275   69.405   54.805
LGA    G    21_A      G    21_A     2.129     0    0.090   0.090     2.129   72.976   72.976
LGA    P    22_A      P    22_A     1.112     0    0.152   0.410     1.914   88.333   82.925
LGA    G    23_A      G    23_A     1.771     0    0.563   0.563     1.771   79.405   79.405
LGA    V    24_A      V    24_A     1.743     0    0.053   0.052     3.502   68.929   61.905
LGA    A    25_A      A    25_A     2.106     0    0.243   0.325     3.503   77.262   70.476
LGA    F    26_A      F    26_A     0.501     0    0.090   0.412     3.421   85.952   76.623
LGA    R    27_A      R    27_A     1.361     0    0.040   1.009     6.482   83.690   49.870
LGA    A    28_A      A    28_A     0.328     0    0.090   0.125     2.005   84.167   85.429
LGA    P    29_A      P    29_A     2.803     0    0.037   0.380     4.805   71.190   56.803
LGA    S    30_A      S    30_A     1.731     0    0.048   0.058     3.934   75.238   64.603
LGA    I    31_A      I    31_A     3.948     0    0.281   1.251    10.484   51.905   29.107
LGA    H    32_A      H    32_A     2.233     0    0.031   0.572     9.617   59.524   29.810
LGA    G    33_A      G    33_A     5.023     0    0.487   0.487     6.724   27.500   27.500

# 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):     2.828          2.586                  3.824           66.140   56.598

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     30    2.42    68.182    63.799     1.191

LGA_LOCAL      RMSD:   2.420  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.862  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   2.828  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.029709 * X  +   0.993635 * Y  +   0.108660 * Z  + -207.449738
  Y_new =  -0.997654 * X  +  -0.036184 * Y  +   0.058117 * Z  + 198.671310
  Z_new =   0.061679 * X  +  -0.106679 * Y  +   0.992379 * Z  + -180.100037 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.600566 -0.061718 -0.107087   [DEG:  -91.7057   -3.5362   -6.1356 ]
ZXZ:  2.061934  0.123540  2.617377   [DEG:  118.1401    7.0783  149.9646 ]
 
# END of job
