
#######################################################
#                                                     #
#                        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   16 (  131),  selected   15 , name one
# Molecule2: number of CA atoms  329 ( 2625),  selected   15 , 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:    15      21_A - 35_A        4.25     4.25
  LCS_AVERAGE:      4.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      23_A - 31_A        1.88     7.51
  LCS_AVERAGE:      2.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4      23_A - 26_A        0.56    11.12
  LONGEST_CONTINUOUS_SEGMENT:     4      25_A - 28_A        0.37     8.80
  LONGEST_CONTINUOUS_SEGMENT:     4      27_A - 30_A        0.63    11.09
  LONGEST_CONTINUOUS_SEGMENT:     4      29_A - 32_A        0.93    12.83
  LCS_AVERAGE:      1.11

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   15
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     M    21_A     M    21_A      3    8   15      4    5    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     N    22_A     N    22_A      3    8   15      4    5    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     K    23_A     K    23_A      4    9   15      3    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     L    24_A     L    24_A      4    9   15      3    5    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     R    25_A     R    25_A      4    9   15      4    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     L    26_A     L    26_A      4    9   15      4    5    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     S    27_A     S    27_A      4    9   15      4    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     V    28_A     V    28_A      4    9   15      4    5    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     A    29_A     A    29_A      4    9   15      3    4    4    6    7    9   10   11   11   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     M    30_A     M    30_A      4    9   15      3    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     G    31_A     G    31_A      4    9   15      3    3    4    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     D    32_A     D    32_A      4    8   15      4    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     Y    33_A     Y    33_A      3    7   15      4    4    5    6    7    9   10   11   12   13   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     D    34_A     D    34_A      3    7   15      3    3    4    6    7    7    9   10   11   12   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     R    35_A     R    35_A      3    7   15      3    3    3    4    5    7    9   10   11   12   13   13   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   2.74  (   1.11    2.55    4.56 )

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      5      6      7      9     10     11     12     13     13     13     15     15     15     15     15     15     15     15 
GDT PERCENT_AT   1.22   1.52   1.52   1.82   2.13   2.74   3.04   3.34   3.65   3.95   3.95   3.95   4.56   4.56   4.56   4.56   4.56   4.56   4.56   4.56
GDT RMS_LOCAL    0.18   0.73   0.67   1.03   1.38   1.88   2.19   2.42   2.75   3.06   3.06   3.06   4.25   4.25   4.25   4.25   4.25   4.25   4.25   4.25
GDT RMS_ALL_AT   4.60   5.99   4.63   4.51   4.53   7.51   7.12   6.51   4.86   5.11   5.11   5.11   4.25   4.25   4.25   4.25   4.25   4.25   4.25   4.25

# Checking swapping
#   possible swapping detected:  Y    33_A      Y    33_A
#   possible swapping detected:  D    34_A      D    34_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M    21_A      M    21_A     2.669     0    0.695   1.736    11.081   71.071   40.119
LGA    N    22_A      N    22_A     1.094     0    0.152   1.137     5.580   73.214   58.214
LGA    K    23_A      K    23_A     2.862     0    0.122   0.895     5.859   71.190   47.566
LGA    L    24_A      L    24_A     1.852     0    0.222   1.172     4.383   65.000   60.476
LGA    R    25_A      R    25_A     1.506     0    0.283   1.397     9.957   75.119   41.991
LGA    L    26_A      L    26_A     2.287     0    0.089   1.436     8.842   73.214   44.226
LGA    S    27_A      S    27_A     2.973     0    0.103   0.658     5.570   67.024   52.619
LGA    V    28_A      V    28_A     1.663     0    0.113   1.165     6.047   61.905   46.054
LGA    A    29_A      A    29_A     3.866     0    0.595   0.576     6.243   57.619   49.524
LGA    M    30_A      M    30_A     1.027     0    0.181   0.871     3.958   72.976   73.810
LGA    G    31_A      G    31_A     3.041     0    0.615   0.615     4.375   50.476   50.476
LGA    D    32_A      D    32_A     6.513     0    0.141   1.108    12.189   13.690    7.440
LGA    Y    33_A      Y    33_A     8.087     0    0.597   1.425    11.852    3.690   16.786
LGA    D    34_A      D    34_A    15.276     0    0.062   1.059    17.176    0.000    0.000
LGA    R    35_A      R    35_A    15.168     0    0.137   1.218    17.692    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       15      60     60  100.00     121    121  100.00               329
SUMMARY(RMSD_GDC):     4.249          4.160                  5.701            2.298    1.791

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   16  329    4.0     11    2.42     2.812     2.861     0.437

LGA_LOCAL      RMSD:   2.418  Number of atoms:   11  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.509  Number of assigned atoms:   15 
Std_ASGN_ATOMS RMSD:   4.249  Standard rmsd on all 15 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.708603 * X  +  -0.636826 * Y  +   0.303866 * Z  +  14.065364
  Y_new =  -0.480496 * X  +  -0.120132 * Y  +   0.868730 * Z  +  21.963629
  Z_new =  -0.516726 * X  +  -0.761591 * Y  +  -0.391119 * Z  + -18.386711 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.595869  0.543022 -2.045229   [DEG:  -34.1408   31.1129 -117.1830 ]
ZXZ:  2.805112  1.972643 -2.545455   [DEG:  160.7211  113.0241 -145.8438 ]
 
# END of job
