
#######################################################
#                                                     #
#                        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:    23       7_A - 29_A        4.85    12.46
  LCS_AVERAGE:     65.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      13_A - 22_A        1.93    12.94
  LCS_AVERAGE:     25.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      27_A - 32_A        0.69    26.02
  LCS_AVERAGE:     13.59

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    8   15      4    4    5    7    8    8    9   10   11   12   12   12   13   14   14   14   14   16   17   20 
LCS_GDT     R     2_A     R     2_A      5    8   15      4    4    5    7    8    8    8    9   10   12   12   12   14   14   15   15   15   16   17   20 
LCS_GDT     Q     3_A     Q     3_A      5    8   15      4    4    5    7    8    8    9   10   11   12   12   12   14   14   15   15   16   19   20   20 
LCS_GDT     S     4_A     S     4_A      5    8   20      4    4    5    7    8    8    8   10   11   12   12   12   14   16   18   19   19   20   20   20 
LCS_GDT     S     5_A     S     5_A      5    8   20      3    4    5    7    8    8    9   10   11   12   15   17   18   18   18   19   19   20   20   20 
LCS_GDT     A     6_A     A     6_A      4    8   21      3    4    5    7    8    8    9   12   16   17   17   17   18   18   18   21   23   24   24   25 
LCS_GDT     T     7_A     T     7_A      4    8   23      3    4    5    7    9   12   14   15   16   17   17   19   21   22   23   23   23   24   24   25 
LCS_GDT     S     8_A     S     8_A      4    8   23      3    4    7    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     S     9_A     S     9_A      3    8   23      3    3    4    7    9   10   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     F    10_A     F    10_A      3    8   23      3    3    4    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    11_A     G    11_A      3    8   23      3    3    4    7    9    9   10   13   16   17   17   17   19   22   23   23   23   24   24   25 
LCS_GDT     G    12_A     G    12_A      3    8   23      3    3    4    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     L    13_A     L    13_A      5   10   23      3    5    7    7    8   10   13   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    14_A     G    14_A      5   10   23      3    5    7    7    8   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    15_A     G    15_A      5   10   23      3    5    7    7    8   11   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    16_A     G    16_A      5   10   23      0    5    5    6    8   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     S    17_A     S    17_A      5   10   23      3    5    5    6    8   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     V    18_A     V    18_A      4   10   23      3    4    6    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     R    19_A     R    19_A      4   10   23      3    4    6    6    8   12   14   15   16   17   17   19   21   21   23   23   23   24   24   25 
LCS_GDT     F    20_A     F    20_A      4   10   23      3    4    6    6    8   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    21_A     G    21_A      4   10   23      2    3    6    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     P    22_A     P    22_A      3   10   23      1    3    5    7    9   12   14   15   16   17   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     G    23_A     G    23_A      4    9   23      3    4    6    6    8   10   12   14   15   16   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     V    24_A     V    24_A      4    9   23      3    4    6    6    8   10   11   14   15   15   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     A    25_A     A    25_A      4    9   23      3    4    7    7    8   10   11   14   15   15   17   20   21   22   23   23   23   24   24   25 
LCS_GDT     F    26_A     F    26_A      4    7   23      3    5    7    7    8    9   11   14   15   15   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     R    27_A     R    27_A      6    7   23      4    5    7    7    8    9   10   14   15   15   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     A    28_A     A    28_A      6    7   23      4    5    6    6    6    8    9   10   11   15   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     P    29_A     P    29_A      6    6   23      4    5    6    6    6    8    9   11   13   15   18   20   21   22   23   23   23   24   24   25 
LCS_GDT     S    30_A     S    30_A      6    6   20      4    5    6    6    6    6    9   11   12   14   15   17   18   19   23   23   23   24   24   25 
LCS_GDT     I    31_A     I    31_A      6    6   19      3    5    6    6    6    6    9    9   11   14   14   16   16   18   18   18   18   19   23   25 
LCS_GDT     H    32_A     H    32_A      6    6   19      3    5    6    6    6    6    8   10   11   14   15   17   17   18   18   20   20   21   23   25 
LCS_GDT     G    33_A     G    33_A      3    6   19      3    3    3    5    5    6    8   11   11   14   15   17   17   18   18   20   20   20   23   25 
LCS_AVERAGE  LCS_A:  34.71  (  13.59   25.16   65.38 )

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      5      7      7      9     12     14     15     16     17     18     20     21     22     23     23     23     24     24     25 
GDT PERCENT_AT  12.12  15.15  21.21  21.21  27.27  36.36  42.42  45.45  48.48  51.52  54.55  60.61  63.64  66.67  69.70  69.70  69.70  72.73  72.73  75.76
GDT RMS_LOCAL    0.23   0.47   1.16   1.16   1.79   2.25   2.44   2.57   2.80   3.10   4.15   4.37   4.52   4.70   4.85   4.85   4.85   5.25   5.25   5.61
GDT RMS_ALL_AT  22.07  25.92  12.96  12.96  14.93  13.74  13.58  13.58  13.80  13.94  12.58  12.36  12.25  12.46  12.46  12.46  12.46  12.33  12.33  12.05

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_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    27.137     0    0.123   0.311    29.755    0.000    0.000
LGA    R     2_A      R     2_A    22.662     0    0.050   0.959    23.725    0.000    0.000
LGA    Q     3_A      Q     3_A    20.288     0    0.085   1.311    25.137    0.000    0.000
LGA    S     4_A      S     4_A    14.047     0    0.077   0.564    16.035    0.000    0.079
LGA    S     5_A      S     5_A    11.426     0    0.557   0.629    12.606    3.214    2.143
LGA    A     6_A      A     6_A     6.672     0    0.072   0.091     8.749   16.190   13.905
LGA    T     7_A      T     7_A     1.404     0    0.138   1.026     5.292   73.452   63.129
LGA    S     8_A      S     8_A     2.349     0    0.610   0.554     3.605   61.667   56.667
LGA    S     9_A      S     9_A     3.614     0    0.738   0.769     6.600   48.452   39.762
LGA    F    10_A      F    10_A     2.821     0    0.672   1.250    10.555   46.905   24.286
LGA    G    11_A      G    11_A     5.442     0    0.139   0.139     5.442   39.524   39.524
LGA    G    12_A      G    12_A     2.178     0    0.383   0.383     4.412   52.500   52.500
LGA    L    13_A      L    13_A     3.657     0    0.509   1.487    10.336   63.452   34.524
LGA    G    14_A      G    14_A     1.299     0    0.051   0.051     2.397   77.381   77.381
LGA    G    15_A      G    15_A     2.971     0    0.611   0.611     2.971   62.976   62.976
LGA    G    16_A      G    16_A     2.505     0    0.648   0.648     3.770   53.690   53.690
LGA    S    17_A      S    17_A     3.053     0    0.187   0.685     6.751   59.405   45.397
LGA    V    18_A      V    18_A     2.032     0    0.118   1.231     5.663   73.095   53.878
LGA    R    19_A      R    19_A     3.413     0    0.028   0.953    15.902   57.500   23.290
LGA    F    20_A      F    20_A     2.658     0    0.538   1.107    10.397   71.190   30.173
LGA    G    21_A      G    21_A     1.575     0    0.200   0.200     3.408   71.429   71.429
LGA    P    22_A      P    22_A     0.970     0    0.639   0.590     5.244   62.619   56.531
LGA    G    23_A      G    23_A     8.351     0    0.599   0.599    10.399    6.905    6.905
LGA    V    24_A      V    24_A    11.318     0    0.089   1.113    13.485    0.119    0.476
LGA    A    25_A      A    25_A    14.898     0    0.252   0.312    17.448    0.000    0.000
LGA    F    26_A      F    26_A    13.123     0    0.050   1.335    15.690    0.000    4.459
LGA    R    27_A      R    27_A    16.347     0    0.028   1.597    19.511    0.000    0.000
LGA    A    28_A      A    28_A    14.377     0    0.154   0.180    17.312    0.000    0.000
LGA    P    29_A      P    29_A    15.368     0    0.093   0.151    17.719    0.000    0.000
LGA    S    30_A      S    30_A    21.247     0    0.070   0.562    24.667    0.000    0.000
LGA    I    31_A      I    31_A    24.933     0    0.618   0.595    28.059    0.000    0.000
LGA    H    32_A      H    32_A    27.611     0    0.069   0.826    30.602    0.000    0.000
LGA    G    33_A      G    33_A    28.079     0    0.318   0.318    29.730    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):    10.394         10.289                 11.426           30.354   24.639

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     15    2.57    37.879    36.606     0.562

LGA_LOCAL      RMSD:   2.569  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.583  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  10.394  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.495475 * X  +  -0.846025 * Y  +  -0.196842 * Z  +  -5.689122
  Y_new =   0.392643 * X  +  -0.420283 * Y  +   0.818043 * Z  + -39.735477
  Z_new =  -0.774814 * X  +   0.328031 * Y  +   0.540425 * Z  +   3.504963 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.471467  0.886420  0.545541   [DEG:  141.6047   50.7882   31.2572 ]
ZXZ: -2.905456  0.999854 -1.170309   [DEG: -166.4704   57.2874  -67.0538 ]
 
# END of job
