
#######################################################
#                                                     #
#                        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:    20       7_A - 26_A        4.80    12.37
  LONGEST_CONTINUOUS_SEGMENT:    20       8_A - 27_A        4.34    12.87
  LONGEST_CONTINUOUS_SEGMENT:    20       9_A - 28_A        4.80    13.01
  LCS_AVERAGE:     57.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      23_A - 33_A        1.96    17.24
  LCS_AVERAGE:     25.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      23_A - 29_A        0.90    16.87
  LCS_AVERAGE:     15.61

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      4    6   19      0    4    4    6    7    9   10   14   16   16   16   17   17   20   20   21   21   22   24   25 
LCS_GDT     R     2_A     R     2_A      4    6   19      3    4    4    6    7    9   10   14   16   16   16   17   17   20   20   21   21   23   24   25 
LCS_GDT     Q     3_A     Q     3_A      4    6   19      3    4    4    6    7    9   10   14   16   16   16   17   17   20   20   21   22   23   24   25 
LCS_GDT     S     4_A     S     4_A      4    6   19      3    4    4    6    7    9   11   14   16   16   16   17   17   18   18   20   22   23   24   25 
LCS_GDT     S     5_A     S     5_A      3    6   19      3    3    5    6    7    9   11   14   16   16   16   17   17   18   18   20   21   23   23   25 
LCS_GDT     A     6_A     A     6_A      3    6   19      3    3    4    6    7    9   11   14   16   16   16   17   17   18   18   20   21   23   23   25 
LCS_GDT     T     7_A     T     7_A      3    6   20      3    3    4    6    7    9   10   14   16   16   16   17   17   18   20   21   21   23   23   25 
LCS_GDT     S     8_A     S     8_A      3    6   20      3    3    3    4    8    8   10   14   16   16   16   18   19   20   20   21   22   23   24   25 
LCS_GDT     S     9_A     S     9_A      5    8   20      3    4    6    6    8    9   11   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     F    10_A     F    10_A      5    8   20      3    4    6    6    8   11   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    11_A     G    11_A      5    8   20      3    4    6    7    8   11   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    12_A     G    12_A      5    8   20      3    4    6    7    8   11   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     L    13_A     L    13_A      5    8   20      3    3    6    8    8   10   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    14_A     G    14_A      3    8   20      3    4    5    6    8   10   11   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    15_A     G    15_A      3    8   20      3    4    5    8    8   11   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    16_A     G    16_A      6    8   20      5    5    6    8    8   11   12   14   16   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     S    17_A     S    17_A      6    7   20      5    5    6    7    8   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     V    18_A     V    18_A      6    7   20      5    5    6    7    8    9   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     R    19_A     R    19_A      6    7   20      5    5    6    7    8    8   11   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     F    20_A     F    20_A      6    7   20      5    5    6    8    8   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    21_A     G    21_A      6    8   20      4    5    6    8    8   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     P    22_A     P    22_A      5    9   20      3    4    6    8    8   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     G    23_A     G    23_A      7   11   20      3    6    7    8    9   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     V    24_A     V    24_A      7   11   20      3    6    7    8    9   11   12   14   15   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     A    25_A     A    25_A      7   11   20      3    6    7    8    9   10   11   12   12   16   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     F    26_A     F    26_A      7   11   20      3    6    7    8    9   10   11   13   14   17   17   18   19   20   20   21   22   23   24   25 
LCS_GDT     R    27_A     R    27_A      7   11   20      3    6    7    8    9   10   11   12   12   13   14   17   18   20   20   21   22   23   24   25 
LCS_GDT     A    28_A     A    28_A      7   11   20      3    6    7    8    9   10   11   12   12   12   13   15   16   17   18   20   21   22   22   25 
LCS_GDT     P    29_A     P    29_A      7   11   15      3    5    7    8    9   10   11   12   13   14   16   16   17   17   18   20   20   22   22   25 
LCS_GDT     S    30_A     S    30_A      6   11   15      3    5    7    8    9   10   11   12   13   14   16   16   17   17   18   20   20   22   22   23 
LCS_GDT     I    31_A     I    31_A      6   11   15      3    5    6    7    9   10   11   12   13   14   16   16   17   17   18   20   20   22   22   23 
LCS_GDT     H    32_A     H    32_A      6   11   15      3    5    6    7    9   10   11   12   13   14   16   16   17   17   18   20   20   22   22   23 
LCS_GDT     G    33_A     G    33_A      3   11   15      3    3    3    7    9   10   11   12   12   12   16   16   17   17   18   19   20   22   22   23 
LCS_AVERAGE  LCS_A:  32.97  (  15.61   25.53   57.76 )

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      6      7      8      9     11     12     14     16     17     17     18     19     20     20     21     22     23     24     25 
GDT PERCENT_AT  15.15  18.18  21.21  24.24  27.27  33.33  36.36  42.42  48.48  51.52  51.52  54.55  57.58  60.61  60.61  63.64  66.67  69.70  72.73  75.76
GDT RMS_LOCAL    0.39   0.66   0.90   1.24   1.39   2.20   2.31   2.72   3.27   3.25   3.25   3.47   4.06   4.34   4.34   4.89   5.29   5.61   5.84   6.33
GDT RMS_ALL_AT  10.56  16.72  16.87  17.07  17.06  13.69  13.74  13.85  16.29  13.42  13.42  13.56  13.00  12.87  12.87  14.21  12.92  13.25  13.54  13.10

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   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    12.667     0    0.596   1.084    15.714    0.000    0.000
LGA    R     2_A      R     2_A    12.292     0    0.592   1.038    18.806    0.000    0.000
LGA    Q     3_A      Q     3_A    11.414     0    0.086   0.710    14.126    0.000    0.000
LGA    S     4_A      S     4_A    12.584     0    0.147   0.555    16.283    0.000    0.000
LGA    S     5_A      S     5_A    16.845     0    0.511   0.764    17.342    0.000    0.000
LGA    A     6_A      A     6_A    16.640     0    0.555   0.570    16.717    0.000    0.000
LGA    T     7_A      T     7_A    16.330     0    0.231   1.121    20.894    0.000    0.000
LGA    S     8_A      S     8_A    11.847     0    0.604   0.546    15.823    1.548    1.032
LGA    S     9_A      S     9_A     5.995     0    0.669   0.944     9.137   19.762   15.079
LGA    F    10_A      F    10_A     2.864     0    0.626   1.233     9.346   61.548   35.974
LGA    G    11_A      G    11_A     1.962     0    0.244   0.244     4.540   54.643   54.643
LGA    G    12_A      G    12_A     1.077     0    0.352   0.352     3.884   72.024   72.024
LGA    L    13_A      L    13_A     4.118     0    0.187   0.312    10.796   56.190   31.012
LGA    G    14_A      G    14_A     5.074     0    0.615   0.615     5.074   43.095   43.095
LGA    G    15_A      G    15_A     2.278     0    0.280   0.280     3.317   71.905   71.905
LGA    G    16_A      G    16_A     2.656     0    0.600   0.600     2.656   71.190   71.190
LGA    S    17_A      S    17_A     1.600     0    0.223   0.250     4.116   67.262   58.254
LGA    V    18_A      V    18_A     3.030     0    0.056   0.100     4.351   61.190   55.578
LGA    R    19_A      R    19_A     4.294     0    0.120   0.720    12.907   49.048   20.563
LGA    F    20_A      F    20_A     1.495     0    0.096   1.183     9.793   62.024   31.515
LGA    G    21_A      G    21_A     2.488     0    0.043   0.043     2.488   66.786   66.786
LGA    P    22_A      P    22_A     2.014     0    0.056   0.408     4.561   68.929   59.320
LGA    G    23_A      G    23_A     3.052     0    0.068   0.068     4.187   54.643   54.643
LGA    V    24_A      V    24_A     3.022     0    0.236   0.996     4.656   45.476   50.952
LGA    A    25_A      A    25_A     6.210     0    0.179   0.201     8.288   27.976   23.333
LGA    F    26_A      F    26_A     5.086     0    0.023   1.282     8.913   17.143   17.316
LGA    R    27_A      R    27_A     8.895     0    0.183   0.970    15.349    4.048    1.948
LGA    A    28_A      A    28_A    14.691     0    0.043   0.058    17.236    0.000    0.000
LGA    P    29_A      P    29_A    17.691     0    0.112   0.271    21.231    0.000    0.000
LGA    S    30_A      S    30_A    23.172     0    0.096   0.143    25.796    0.000    0.000
LGA    I    31_A      I    31_A    30.479     0    0.614   1.479    34.723    0.000    0.000
LGA    H    32_A      H    32_A    33.284     0    0.067   1.157    34.968    0.000    0.000
LGA    G    33_A      G    33_A    36.732     0    0.514   0.514    38.566    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):     9.335          9.258                  9.733           29.589   25.338

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.72    37.121    35.409     0.497

LGA_LOCAL      RMSD:   2.719  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.848  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.335  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.015678 * X  +  -0.543746 * Y  +   0.839104 * Z  +  -3.166076
  Y_new =  -0.049404 * X  +   0.838603 * Y  +   0.542498 * Z  + -40.003796
  Z_new =  -0.998656 * X  +  -0.032950 * Y  +  -0.040011 * Z  +  41.100868 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.878080  1.518941 -2.452666   [DEG: -107.6060   87.0289 -140.5274 ]
ZXZ:  2.144722  1.610818 -1.603779   [DEG:  122.8835   92.2931  -91.8898 ]
 
# END of job
