
#######################################################
#                                                     #
#                        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       5_A - 27_A        4.87    12.36
  LONGEST_CONTINUOUS_SEGMENT:    23       6_A - 28_A        4.56    12.24
  LONGEST_CONTINUOUS_SEGMENT:    23       7_A - 29_A        4.96    11.67
  LCS_AVERAGE:     64.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      12_A - 23_A        1.93    11.86
  LCS_AVERAGE:     27.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      25_A - 30_A        0.78    18.60
  LCS_AVERAGE:     13.41

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    7   13      3    4    4    6    7    7    9   10   11   12   12   12   12   13   13   13   13   13   15   15 
LCS_GDT     R     2_A     R     2_A      4    7   13      3    4    4    6    7    7    9   10   11   12   12   12   12   13   16   17   18   19   21   21 
LCS_GDT     Q     3_A     Q     3_A      4    7   13      3    4    4    6    7    7    9   10   11   12   12   12   12   13   16   17   18   19   21   21 
LCS_GDT     S     4_A     S     4_A      4    7   13      3    4    4    5    7    7    9   10   11   12   12   12   12   13   16   17   18   19   21   21 
LCS_GDT     S     5_A     S     5_A      4    7   23      3    4    4    6    7    7    9   10   11   12   12   12   12   14   19   20   20   21   23   26 
LCS_GDT     A     6_A     A     6_A      4    7   23      3    4    4    6    7    7   10   10   11   14   17   18   20   22   22   23   23   26   26   27 
LCS_GDT     T     7_A     T     7_A      4    7   23      3    4    6    8   11   12   15   16   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     S     8_A     S     8_A      4    6   23      3    5    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     S     9_A     S     9_A      3    5   23      2    3    3    7    8   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     F    10_A     F    10_A      3    6   23      0    3    3    5    6    9   11   15   16   18   19   21   21   22   22   22   23   24   26   27 
LCS_GDT     G    11_A     G    11_A      3    6   23      3    3    3    4    8   10   16   17   18   18   19   21   21   22   22   22   23   24   24   25 
LCS_GDT     G    12_A     G    12_A      3   12   23      3    3    3    4    7   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     L    13_A     L    13_A      5   12   23      3    5    7    8   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     G    14_A     G    14_A      5   12   23      3    5    7    8   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     G    15_A     G    15_A      5   12   23      3    4    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     G    16_A     G    16_A      5   12   23      3    5    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     S    17_A     S    17_A      5   12   23      3    5    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     V    18_A     V    18_A      4   12   23      3    4    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     R    19_A     R    19_A      4   12   23      3    5    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     F    20_A     F    20_A      4   12   23      3    4    6    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     G    21_A     G    21_A      4   12   23      3    4    6    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     P    22_A     P    22_A      4   12   23      3    5    7    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     G    23_A     G    23_A      5   12   23      3    5    8    8   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     V    24_A     V    24_A      5   10   23      3    4    8    9   11   13   16   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     A    25_A     A    25_A      6    9   23      3    5    8    8    8    9   10   12   13   15   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     F    26_A     F    26_A      6    9   23      3    5    8    8    9   12   15   17   18   18   19   21   21   22   22   23   23   26   26   27 
LCS_GDT     R    27_A     R    27_A      6    9   23      3    5    8    8    8    9   10   12   13   15   18   21   21   22   22   23   23   26   26   27 
LCS_GDT     A    28_A     A    28_A      6    9   23      3    5    8    8    8    9   10   12   13   14   17   17   18   20   22   23   23   26   26   27 
LCS_GDT     P    29_A     P    29_A      6    9   23      3    5    8    8    8    9   10   12   13   14   17   17   18   20   22   23   23   26   26   27 
LCS_GDT     S    30_A     S    30_A      6    9   19      3    5    8    8    8    9   10   12   13   14   17   17   18   20   21   23   23   26   26   27 
LCS_GDT     I    31_A     I    31_A      4    9   18      3    3    6    7    8    9   10   12   13   14   17   17   18   20   21   22   23   26   26   27 
LCS_GDT     H    32_A     H    32_A      4    8   18      3    3    6    7    8    9   10   12   13   14   17   17   18   20   21   22   23   26   26   27 
LCS_GDT     G    33_A     G    33_A      3    4   18      3    3    3    3    4    6    8   11   13   14   17   17   18   19   21   22   22   26   26   27 
LCS_AVERAGE  LCS_A:  35.11  (  13.41   27.64   64.28 )

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      3      5      8      9     11     13     16     17     18     18     19     21     21     22     22     23     23     26     26     27 
GDT PERCENT_AT   9.09  15.15  24.24  27.27  33.33  39.39  48.48  51.52  54.55  54.55  57.58  63.64  63.64  66.67  66.67  69.70  69.70  78.79  78.79  81.82
GDT RMS_LOCAL    0.05   0.52   1.01   1.39   1.64   2.12   2.53   2.64   2.82   2.82   3.06   3.52   3.52   3.91   3.91   5.43   4.56   6.33   6.33   6.52
GDT RMS_ALL_AT  18.46  18.28  18.97  13.02  12.98  13.07  13.54  13.43  13.20  13.20  13.29  13.12  13.12  12.82  12.82  10.42  12.24   9.46   9.46   9.47

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_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    33.463     0    0.141   1.178    35.040    0.000    0.000
LGA    R     2_A      R     2_A    26.512     0    0.070   1.083    29.240    0.000    0.000
LGA    Q     3_A      Q     3_A    23.181     0    0.122   1.068    23.964    0.000    0.000
LGA    S     4_A      S     4_A    20.658     0    0.198   0.567    21.723    0.000    0.000
LGA    S     5_A      S     5_A    16.000     0    0.554   0.836    17.727    0.000    0.000
LGA    A     6_A      A     6_A     9.138     0    0.082   0.086    11.498    2.857    2.571
LGA    T     7_A      T     7_A     5.271     0    0.052   1.031     5.874   37.024   31.701
LGA    S     8_A      S     8_A     2.653     0    0.614   0.854     4.249   61.667   58.095
LGA    S     9_A      S     9_A     3.237     0    0.699   0.758     7.176   41.071   37.143
LGA    F    10_A      F    10_A     5.843     0    0.694   1.090     9.478   34.762   14.935
LGA    G    11_A      G    11_A     3.982     0    0.195   0.195     4.571   51.071   51.071
LGA    G    12_A      G    12_A     2.971     0    0.211   0.211     2.971   64.881   64.881
LGA    L    13_A      L    13_A     2.562     0    0.044   0.957     5.482   53.690   47.262
LGA    G    14_A      G    14_A     2.627     0    0.482   0.482     2.627   67.024   67.024
LGA    G    15_A      G    15_A     1.667     0    0.198   0.198     1.667   83.810   83.810
LGA    G    16_A      G    16_A     2.349     0    0.599   0.599     2.349   68.810   68.810
LGA    S    17_A      S    17_A     2.491     0    0.133   0.121     3.268   57.262   58.492
LGA    V    18_A      V    18_A     3.236     0    0.050   1.073     5.577   63.333   53.605
LGA    R    19_A      R    19_A     1.557     0    0.124   0.726     3.523   70.952   61.212
LGA    F    20_A      F    20_A     2.053     0    0.190   0.286     8.323   79.524   40.693
LGA    G    21_A      G    21_A     2.516     0    0.201   0.201     2.516   69.048   69.048
LGA    P    22_A      P    22_A     1.516     0    0.090   0.283     2.516   79.405   73.197
LGA    G    23_A      G    23_A     1.654     0    0.143   0.143     4.072   64.048   64.048
LGA    V    24_A      V    24_A     2.290     0    0.078   1.074     5.307   65.119   54.286
LGA    A    25_A      A    25_A     6.141     0    0.228   0.280     9.025   27.857   22.571
LGA    F    26_A      F    26_A     3.865     0    0.069   1.405     7.938   25.833   23.723
LGA    R    27_A      R    27_A     7.318     0    0.115   1.066     8.828   10.952   19.524
LGA    A    28_A      A    28_A    13.390     0    0.035   0.041    16.095    0.000    0.000
LGA    P    29_A      P    29_A    15.461     0    0.679   0.621    18.285    0.000    0.000
LGA    S    30_A      S    30_A    19.376     0    0.072   0.547    20.489    0.000    0.000
LGA    I    31_A      I    31_A    22.918     0    0.622   1.513    26.488    0.000    0.000
LGA    H    32_A      H    32_A    23.067     0    0.044   1.374    24.661    0.000    0.000
LGA    G    33_A      G    33_A    26.536     0    0.583   0.583    30.404    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):     9.014          8.866                  9.616           35.758   32.355

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     17    2.64    40.909    39.791     0.620

LGA_LOCAL      RMSD:   2.644  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.432  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.014  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.361848 * X  +   0.225197 * Y  +  -0.904628 * Z  + -19.321468
  Y_new =  -0.165802 * X  +  -0.939367 * Y  +  -0.300165 * Z  +   5.617892
  Z_new =  -0.917374 * X  +   0.258604 * Y  +  -0.302570 * Z  +  -1.025500 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.429660  1.161433  2.434382   [DEG:  -24.6177   66.5452  139.4798 ]
ZXZ: -1.250417  1.878184 -1.296031   [DEG:  -71.6436  107.6120  -74.2571 ]
 
# END of job
