
#######################################################
#                                                     #
#                        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:    18      14_A - 31_A        4.98    19.25
  LONGEST_CONTINUOUS_SEGMENT:    18      15_A - 32_A        4.87    19.70
  LCS_AVERAGE:     48.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      24_A - 32_A        1.60    19.99
  LONGEST_CONTINUOUS_SEGMENT:     9      25_A - 33_A        1.78    23.83
  LCS_AVERAGE:     23.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.96    21.82
  LCS_AVERAGE:     14.42

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   12      3    5    6    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   12 
LCS_GDT     R     2_A     R     2_A      5    8   12      4    5    6    7    8    8    8    8    9    9    9   10   10   11   12   12   12   12   12   12 
LCS_GDT     Q     3_A     Q     3_A      5    8   12      4    5    5    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   12 
LCS_GDT     S     4_A     S     4_A      5    8   12      4    5    6    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   12 
LCS_GDT     S     5_A     S     5_A      5    8   12      4    5    6    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   12 
LCS_GDT     A     6_A     A     6_A      5    8   12      3    4    6    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   12 
LCS_GDT     T     7_A     T     7_A      5    8   12      3    4    6    7    8    8    8    8    9    9    9   10   11   11   12   12   12   12   12   13 
LCS_GDT     S     8_A     S     8_A      3    8   12      3    3    3    6    8    8    8    8    9    9   10   10   11   11   12   12   12   12   12   14 
LCS_GDT     S     9_A     S     9_A      3    5   12      3    3    3    4    5    5    7    8    9    9   10   10   11   11   12   12   12   12   12   14 
LCS_GDT     F    10_A     F    10_A      3    5   12      3    3    3    4    5    6    6    8    8    9   10   10   11   11   12   12   12   13   15   15 
LCS_GDT     G    11_A     G    11_A      3    5   12      3    3    3    4    5    5    7    8    8    9   10   10   11   12   13   15   18   19   20   23 
LCS_GDT     G    12_A     G    12_A      3    5   15      1    3    3    4    5    6    6    8    8    9   10   12   15   16   18   19   21   21   22   23 
LCS_GDT     L    13_A     L    13_A      4    5   17      3    4    4    4    5    6    7    9   10   10   13   15   16   18   19   20   21   21   22   23 
LCS_GDT     G    14_A     G    14_A      4    5   18      3    4    4    4    6    9   10   10   11   12   13   15   16   19   19   20   21   21   22   23 
LCS_GDT     G    15_A     G    15_A      4    7   18      3    4    4    5    7    9   10   11   11   12   13   15   17   19   19   20   21   21   22   23 
LCS_GDT     G    16_A     G    16_A      4    8   18      0    4    4    5    7    9   10   11   11   12   13   14   16   19   19   20   21   21   22   23 
LCS_GDT     S    17_A     S    17_A      5    8   18      3    4    5    5    7    9   10   11   11   12   13   14   17   19   19   20   21   21   22   23 
LCS_GDT     V    18_A     V    18_A      5    8   18      4    4    5    5    7    9   10   11   12   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     R    19_A     R    19_A      5    8   18      4    4    5    5    7    9   10   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     F    20_A     F    20_A      5    8   18      4    4    5    5    7    9   10   11   11   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     G    21_A     G    21_A      5    8   18      4    4    5    5    7    9   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     P    22_A     P    22_A      4    8   18      3    4    4    5    7    9   10   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     G    23_A     G    23_A      4    8   18      3    4    4    6    7   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     V    24_A     V    24_A      3    9   18      3    3    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     A    25_A     A    25_A      3    9   18      3    4    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     F    26_A     F    26_A      7    9   18      4    5    7    8    9   10   11   12   13   13   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     R    27_A     R    27_A      7    9   18      4    5    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     A    28_A     A    28_A      7    9   18      4    5    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     P    29_A     P    29_A      7    9   18      4    5    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     S    30_A     S    30_A      7    9   18      3    4    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     I    31_A     I    31_A      7    9   18      3    5    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     H    32_A     H    32_A      7    9   18      3    4    7    8    9   10   11   12   13   14   14   15   17   19   19   20   21   21   22   23 
LCS_GDT     G    33_A     G    33_A      3    9   17      3    3    3    3    7    9    9   10   10   11   11   13   13   15   16   17   18   21   22   23 
LCS_AVERAGE  LCS_A:  28.62  (  14.42   23.42   48.03 )

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      8      9     10     11     12     13     14     14     15     17     19     19     20     21     21     22     23 
GDT PERCENT_AT  12.12  15.15  21.21  24.24  27.27  30.30  33.33  36.36  39.39  42.42  42.42  45.45  51.52  57.58  57.58  60.61  63.64  63.64  66.67  69.70
GDT RMS_LOCAL    0.24   0.63   0.96   1.33   1.60   2.23   2.45   2.68   3.02   3.70   3.29   3.79   4.56   5.06   5.06   5.29   5.68   5.68   5.96   6.49
GDT RMS_ALL_AT  25.39  31.78  21.82  19.30  19.99  26.69  27.23  27.76  23.57  20.98  23.52  21.55  20.16  19.25  19.25  18.71  18.10  18.10  18.13  17.58

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_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    46.251     0    0.535   0.780    53.656    0.000    0.000
LGA    R     2_A      R     2_A    47.252     0    0.055   1.418    59.726    0.000    0.000
LGA    Q     3_A      Q     3_A    45.241     0    0.089   0.166    47.186    0.000    0.000
LGA    S     4_A      S     4_A    46.968     0    0.019   0.027    48.947    0.000    0.000
LGA    S     5_A      S     5_A    46.137     0    0.347   0.393    46.863    0.000    0.000
LGA    A     6_A      A     6_A    46.601     0    0.378   0.423    46.641    0.000    0.000
LGA    T     7_A      T     7_A    45.756     0    0.030   1.128    47.029    0.000    0.000
LGA    S     8_A      S     8_A    42.975     0    0.566   0.734    44.740    0.000    0.000
LGA    S     9_A      S     9_A    35.671     0    0.070   0.652    38.309    0.000    0.000
LGA    F    10_A      F    10_A    33.877     0    0.203   1.237    37.494    0.000    0.000
LGA    G    11_A      G    11_A    35.065     0    0.627   0.627    35.092    0.000    0.000
LGA    G    12_A      G    12_A    33.490     0    0.588   0.588    34.390    0.000    0.000
LGA    L    13_A      L    13_A    30.764     0    0.648   0.561    31.955    0.000    0.000
LGA    G    14_A      G    14_A    30.529     0    0.199   0.199    30.567    0.000    0.000
LGA    G    15_A      G    15_A    24.326     0    0.611   0.611    26.496    0.000    0.000
LGA    G    16_A      G    16_A    22.706     0    0.562   0.562    23.736    0.000    0.000
LGA    S    17_A      S    17_A    17.157     0    0.226   0.661    19.139    0.000    0.000
LGA    V    18_A      V    18_A    15.363     0    0.117   1.097    18.796    0.000    0.000
LGA    R    19_A      R    19_A     8.823     0    0.058   1.432    13.071    1.429    2.814
LGA    F    20_A      F    20_A     7.623     0    0.032   0.235    16.404   21.667    8.009
LGA    G    21_A      G    21_A     3.410     0    0.041   0.041     5.297   45.833   45.833
LGA    P    22_A      P    22_A     3.953     0    0.468   0.666     5.544   42.500   38.231
LGA    G    23_A      G    23_A     2.715     0    0.290   0.290     3.999   61.548   61.548
LGA    V    24_A      V    24_A     2.307     0    0.559   1.002     6.947   77.381   54.354
LGA    A    25_A      A    25_A     2.090     0    0.146   0.184     4.677   59.881   54.190
LGA    F    26_A      F    26_A     2.096     0    0.109   1.288     7.503   75.357   41.255
LGA    R    27_A      R    27_A     3.379     0    0.020   0.730    14.046   57.500   24.242
LGA    A    28_A      A    28_A     1.858     0    0.011   0.011     4.332   79.405   70.952
LGA    P    29_A      P    29_A     3.004     0    0.666   0.589     6.666   67.262   48.571
LGA    S    30_A      S    30_A     0.426     0    0.165   0.288     3.247   76.071   72.381
LGA    I    31_A      I    31_A     3.178     0    0.601   0.988     6.782   52.262   38.393
LGA    H    32_A      H    32_A     1.899     0    0.571   0.987     7.854   50.000   32.762
LGA    G    33_A      G    33_A     7.946     0    0.524   0.524     9.798    8.571    8.571

# 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):    14.644         14.478                 15.584           23.535   18.246

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     12    2.68    34.091    31.944     0.431

LGA_LOCAL      RMSD:   2.685  Number of atoms:   12  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  27.764  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  14.644  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.018460 * X  +   0.157439 * Y  +   0.987356 * Z  +  32.628826
  Y_new =   0.783209 * X  +  -0.616113 * Y  +   0.083599 * Z  +  32.300312
  Z_new =   0.621485 * X  +   0.771763 * Y  +  -0.134681 * Z  +  -0.503596 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.547231 -0.670637  1.743567   [DEG:   88.6498  -38.4247   99.8991 ]
ZXZ:  1.655265  1.705888  0.677952   [DEG:   94.8397   97.7402   38.8438 ]
 
# END of job
