
#######################################################
#                                                     #
#                        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      12_A - 32_A        4.83    16.32
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.67    16.89
  LCS_AVERAGE:     53.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      14_A - 24_A        1.98    17.94
  LONGEST_CONTINUOUS_SEGMENT:    11      15_A - 25_A        1.97    18.35
  LONGEST_CONTINUOUS_SEGMENT:    11      18_A - 28_A        1.72    17.07
  LONGEST_CONTINUOUS_SEGMENT:    11      20_A - 30_A        2.00    17.14
  LCS_AVERAGE:     27.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      18_A - 24_A        0.76    17.95
  LONGEST_CONTINUOUS_SEGMENT:     7      20_A - 26_A        0.94    16.44
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.98    20.24
  LCS_AVERAGE:     16.71

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   11      4    4    5    6    6    8    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     R     2_A     R     2_A      5    7   11      4    4    5    6    6    8    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     Q     3_A     Q     3_A      5    7   11      4    4    5    6    6    8    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     S     4_A     S     4_A      5    7   11      4    4    5    6    6    8    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    6    6    8    8    8    8    9    9    9    9   10   11   11   12   12   14   14 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    4    6    6    8    8    8    8    9   10   10   11   12   12   12   13   13   14   14 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    4    5    8    8    8    9    9   10   10   11   12   12   12   13   14   14   16 
LCS_GDT     S     8_A     S     8_A      4    6   11      3    4    4    4    5    8    8    8    9    9   10   10   11   12   13   13   13   14   15   16 
LCS_GDT     S     9_A     S     9_A      4    7   11      4    4    4    5    6    6    7    8    9    9   10   10   11   12   13   13   13   14   14   16 
LCS_GDT     F    10_A     F    10_A      4    7   11      4    4    4    5    6    6    7    8    9    9   10   10   11   12   13   13   13   14   15   18 
LCS_GDT     G    11_A     G    11_A      4    7   15      4    4    4    5    6    6    7    8    9    9   10   11   11   14   16   17   17   18   19   20 
LCS_GDT     G    12_A     G    12_A      4    7   21      4    4    4    5    5    6    7    9   10   14   15   15   16   17   19   19   20   20   21   22 
LCS_GDT     L    13_A     L    13_A      4    7   21      4    4    4    5    6    6    8   11   15   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    14_A     G    14_A      4   11   21      4    4    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    15_A     G    15_A      3   11   21      3    4    6    9   10   11   12   13   16   16   16   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    16_A     G    16_A      5   11   21      3    4    6    8    9   10   11   13   13   14   15   16   18   18   19   20   20   20   21   22 
LCS_GDT     S    17_A     S    17_A      5   11   21      3    4    6    8    9   11   12   13   14   14   15   17   18   18   19   20   20   20   21   22 
LCS_GDT     V    18_A     V    18_A      7   11   21      5    7    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     R    19_A     R    19_A      7   11   21      5    7    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     F    20_A     F    20_A      7   11   21      5    7    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    21_A     G    21_A      7   11   21      5    7    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     P    22_A     P    22_A      7   11   21      5    7    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    23_A     G    23_A      7   11   21      4    7    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     V    24_A     V    24_A      7   11   21      4    7    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     A    25_A     A    25_A      7   11   21      4    5    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     F    26_A     F    26_A      7   11   21      5    5    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     R    27_A     R    27_A      7   11   21      5    5    8    9   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     A    28_A     A    28_A      7   11   21      5    5    6    9   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     P    29_A     P    29_A      7   11   21      5    5    6    7   10   11   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     S    30_A     S    30_A      7   11   21      5    5    6    7   10   11   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     I    31_A     I    31_A      7    9   21      3    3    6    7    8   10   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     H    32_A     H    32_A      7    9   21      3    5    6    7    8    9   13   13   14   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    33_A     G    33_A      3    8   21      3    3    3    4    4    7    8    8    9   10   12   12   16   16   19   19   20   20   21   22 
LCS_AVERAGE  LCS_A:  32.81  (  16.71   27.82   53.90 )

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      7      8     10     10     12     14     15     16     16     17     17     18     18     19     20     20     20     21     22 
GDT PERCENT_AT  15.15  21.21  24.24  30.30  30.30  36.36  42.42  45.45  48.48  48.48  51.52  51.52  54.55  54.55  57.58  60.61  60.61  60.61  63.64  66.67
GDT RMS_LOCAL    0.29   0.76   1.11   1.33   1.33   1.85   2.52   2.67   2.89   2.89   3.29   3.29   3.53   3.53   3.88   4.18   4.18   4.18   4.67   5.18
GDT RMS_ALL_AT  18.65  17.95  16.35  17.17  17.17  16.97  16.89  16.96  17.04  17.04  16.45  16.45  16.57  16.57  16.78  16.96  16.96  16.96  16.89  16.31

# 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    27.695     0    0.023   0.817    29.411    0.000    0.000
LGA    R     2_A      R     2_A    29.673     0    0.097   1.080    33.963    0.000    0.000
LGA    Q     3_A      Q     3_A    29.750     0    0.174   0.721    30.949    0.000    0.000
LGA    S     4_A      S     4_A    30.613     0    0.205   0.641    32.102    0.000    0.000
LGA    S     5_A      S     5_A    32.041     0    0.541   0.561    34.397    0.000    0.000
LGA    A     6_A      A     6_A    31.776     0    0.220   0.259    31.776    0.000    0.000
LGA    T     7_A      T     7_A    31.159     0    0.252   0.352    34.241    0.000    0.000
LGA    S     8_A      S     8_A    28.499     0    0.372   0.693    29.432    0.000    0.000
LGA    S     9_A      S     9_A    27.463     0    0.447   0.748    29.443    0.000    0.000
LGA    F    10_A      F    10_A    20.919     0    0.501   1.051    23.270    0.000    0.000
LGA    G    11_A      G    11_A    18.497     0    0.382   0.382    19.641    0.000    0.000
LGA    G    12_A      G    12_A    13.035     0    0.078   0.078    15.272    0.000    0.000
LGA    L    13_A      L    13_A     7.120     0    0.135   0.248    12.419   20.357   10.774
LGA    G    14_A      G    14_A     3.267     0    0.555   0.555     4.372   41.905   41.905
LGA    G    15_A      G    15_A     5.636     0    0.265   0.265     7.555   18.333   18.333
LGA    G    16_A      G    16_A     8.482     0    0.609   0.609     8.482    9.762    9.762
LGA    S    17_A      S    17_A     7.628     0    0.119   0.624    11.496   10.595    7.540
LGA    V    18_A      V    18_A     3.312     0    0.215   0.969     4.742   45.357   50.612
LGA    R    19_A      R    19_A     2.913     0    0.224   0.785     8.482   53.571   35.368
LGA    F    20_A      F    20_A     1.685     0    0.137   0.298     2.840   79.405   69.481
LGA    G    21_A      G    21_A     1.371     0    0.081   0.081     2.036   72.976   72.976
LGA    P    22_A      P    22_A     1.411     0    0.617   0.789     4.272   66.190   76.599
LGA    G    23_A      G    23_A     1.636     0    0.632   0.632     2.120   77.381   77.381
LGA    V    24_A      V    24_A     0.283     0    0.102   0.979     1.624   83.929   82.925
LGA    A    25_A      A    25_A     2.758     0    0.000   0.012     3.609   59.286   56.095
LGA    F    26_A      F    26_A     3.169     0    0.167   1.286     4.242   51.786   55.152
LGA    R    27_A      R    27_A     3.331     0    0.006   0.947     6.940   57.381   35.498
LGA    A    28_A      A    28_A     2.082     0    0.034   0.033     2.769   66.786   64.857
LGA    P    29_A      P    29_A     2.963     0    0.027   0.342     3.963   60.952   55.374
LGA    S    30_A      S    30_A     3.384     0    0.074   0.650     5.397   42.381   37.857
LGA    I    31_A      I    31_A     3.694     0    0.627   0.488     7.034   38.333   34.583
LGA    H    32_A      H    32_A     6.986     0    0.051   1.426     9.694   10.714    7.476
LGA    G    33_A      G    33_A    11.328     0    0.514   0.514    12.841    0.119    0.119

# 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):    12.841         12.731                 13.051           29.318   27.293

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     15    2.67    39.394    36.953     0.542

LGA_LOCAL      RMSD:   2.665  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.957  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  12.841  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.603186 * X  +  -0.784832 * Y  +   0.142146 * Z  + -42.534622
  Y_new =  -0.797044 * X  +  -0.586460 * Y  +   0.144169 * Z  +  35.359116
  Z_new =  -0.029785 * X  +  -0.200258 * Y  +  -0.979290 * Z  + -81.337822 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.922971  0.029790 -2.939881   [DEG:  -52.8824    1.7068 -168.4428 ]
ZXZ:  2.363259  2.937722 -2.993940   [DEG:  135.4048  168.3191 -171.5401 ]
 
# END of job
