
#######################################################
#                                                     #
#                        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:    21      13_A - 33_A        4.78    17.48
  LCS_AVERAGE:     54.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      15_A - 23_A        1.92    18.83
  LCS_AVERAGE:     23.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       1_A - 5_A         0.75    32.81
  LONGEST_CONTINUOUS_SEGMENT:     5       2_A - 6_A         0.95    30.98
  LONGEST_CONTINUOUS_SEGMENT:     5       3_A - 7_A         0.97    31.10
  LONGEST_CONTINUOUS_SEGMENT:     5      17_A - 21_A        0.99    26.71
  LONGEST_CONTINUOUS_SEGMENT:     5      29_A - 33_A        0.89    15.97
  LCS_AVERAGE:     13.50

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   11      3    4    5    7    8    8    8    8    9    9    9    9    9   11   11   11   12   12   12   13 
LCS_GDT     R     2_A     R     2_A      5    8   11      4    4    5    7    8    8    8    8    9    9    9    9    9   11   11   11   12   12   12   13 
LCS_GDT     Q     3_A     Q     3_A      5    8   11      4    4    5    7    8    8    8    8    9    9    9    9    9   11   11   11   12   12   12   13 
LCS_GDT     S     4_A     S     4_A      5    8   11      4    4    5    7    8    8    8    8    9    9    9    9    9   11   11   11   12   12   12   13 
LCS_GDT     S     5_A     S     5_A      5    8   13      4    4    5    7    8    8    8    8    9    9   10   11   11   12   13   13   14   14   14   14 
LCS_GDT     A     6_A     A     6_A      5    8   13      3    4    5    7    8    8    8    8    9   10   10   11   11   12   13   13   15   16   17   17 
LCS_GDT     T     7_A     T     7_A      5    8   13      3    4    5    7    8    8    8    8   10   10   11   11   12   13   14   14   15   16   17   17 
LCS_GDT     S     8_A     S     8_A      3    8   13      3    3    5    6    8    8    9    9   10   10   11   12   13   13   14   14   15   16   17   17 
LCS_GDT     S     9_A     S     9_A      4    6   13      3    4    4    4    6    8    9    9   10   10   11   12   13   13   14   14   15   16   17   17 
LCS_GDT     F    10_A     F    10_A      4    6   13      3    4    4    4    6    8    9    9   10   10   11   12   13   13   14   14   15   16   17   20 
LCS_GDT     G    11_A     G    11_A      4    6   13      3    4    4    4    6    8    9    9   10   10   11   12   15   17   17   18   21   23   23   23 
LCS_GDT     G    12_A     G    12_A      4    6   16      3    4    4    4    6    8    9    9   10   10   13   16   16   17   21   22   22   23   23   23 
LCS_GDT     L    13_A     L    13_A      4    5   21      3    4    4    4    6    8    9    9   10   10   11   16   18   21   21   22   22   23   23   23 
LCS_GDT     G    14_A     G    14_A      4    5   21      3    4    4    5    6    8    9   10   11   14   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     G    15_A     G    15_A      4    9   21      3    4    4    4    7    9   10   10   12   14   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     G    16_A     G    16_A      4    9   21      0    4    4    5    7    9   10   10   12   14   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     S    17_A     S    17_A      5    9   21      3    4    5    5    7    9   10   11   12   13   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     V    18_A     V    18_A      5    9   21      4    4    5    5    7    9   10   12   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     R    19_A     R    19_A      5    9   21      4    4    5    7   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     F    20_A     F    20_A      5    9   21      4    4    5    5    7    9   10   11   13   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     G    21_A     G    21_A      5    9   21      4    4    5    7   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     P    22_A     P    22_A      4    9   21      4    5    5    7   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     G    23_A     G    23_A      4    9   21      3    4    6    7   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     V    24_A     V    24_A      4    7   21      3    3    6    8   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     A    25_A     A    25_A      4    8   21      3    4    6    8   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     F    26_A     F    26_A      4    8   21      3    3    4    7    9   10   13   14   14   16   16   18   19   21   21   22   22   23   23   23 
LCS_GDT     R    27_A     R    27_A      4    8   21      3    3    5    8    9   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     A    28_A     A    28_A      3    8   21      3    4    6    8   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     P    29_A     P    29_A      5    8   21      3    4    5    7   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     S    30_A     S    30_A      5    8   21      4    5    6    8   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     I    31_A     I    31_A      5    8   21      3    5    6    8   10   11   13   14   14   16   17   18   19   21   21   22   22   23   23   23 
LCS_GDT     H    32_A     H    32_A      5    8   21      4    5    6    8    9   11   13   14   14   16   16   17   19   21   21   22   22   23   23   23 
LCS_GDT     G    33_A     G    33_A      5    7   21      4    5    6    8    9    9   12   14   14   16   16   16   19   21   21   22   22   23   23   23 
LCS_AVERAGE  LCS_A:  30.49  (  13.50   23.60   54.36 )

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      6      8     10     11     13     14     14     16     17     18     19     21     21     22     22     23     23     23 
GDT PERCENT_AT  12.12  15.15  18.18  24.24  30.30  33.33  39.39  42.42  42.42  48.48  51.52  54.55  57.58  63.64  63.64  66.67  66.67  69.70  69.70  69.70
GDT RMS_LOCAL    0.26   0.55   0.91   1.22   1.94   2.06   2.37   2.59   2.59   3.19   4.10   4.22   4.34   4.78   4.78   5.16   5.16   5.67   5.67   5.67
GDT RMS_ALL_AT  16.22  16.22  16.45  19.69  20.43  20.08  20.45  19.42  19.42  18.97  17.91  18.06  17.83  17.48  17.48  16.98  16.98  16.51  16.51  16.51

# Checking swapping
#   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    38.946     0    0.131   1.120    47.257    0.000    0.000
LGA    R     2_A      R     2_A    36.131     0    0.039   0.883    37.588    0.000    0.000
LGA    Q     3_A      Q     3_A    35.810     0    0.113   0.978    37.797    0.000    0.000
LGA    S     4_A      S     4_A    35.227     0    0.020   0.030    35.393    0.000    0.000
LGA    S     5_A      S     5_A    35.740     0    0.383   0.421    36.243    0.000    0.000
LGA    A     6_A      A     6_A    35.269     0    0.479   0.513    35.707    0.000    0.000
LGA    T     7_A      T     7_A    33.886     0    0.048   1.088    38.446    0.000    0.000
LGA    S     8_A      S     8_A    28.930     0    0.620   0.827    30.560    0.000    0.000
LGA    S     9_A      S     9_A    26.240     0    0.189   0.686    28.730    0.000    0.000
LGA    F    10_A      F    10_A    18.850     0    0.201   1.107    21.714    0.000    0.000
LGA    G    11_A      G    11_A    17.577     0    0.542   0.542    18.608    0.000    0.000
LGA    G    12_A      G    12_A    16.876     0    0.573   0.573    17.065    0.000    0.000
LGA    L    13_A      L    13_A    15.398     0    0.073   1.417    16.320    0.000    0.000
LGA    G    14_A      G    14_A    14.387     0    0.216   0.216    14.387    0.000    0.000
LGA    G    15_A      G    15_A    10.938     0    0.643   0.643    11.789    0.714    0.714
LGA    G    16_A      G    16_A    11.731     0    0.538   0.538    11.973    0.000    0.000
LGA    S    17_A      S    17_A     9.019     0    0.215   0.660     9.638    5.595    5.317
LGA    V    18_A      V    18_A     6.866     0    0.117   1.095    10.890   13.810    8.299
LGA    R    19_A      R    19_A     2.882     0    0.063   1.142    13.814   43.810   25.541
LGA    F    20_A      F    20_A     5.821     0    0.114   1.149    13.264   26.429    9.870
LGA    G    21_A      G    21_A     2.580     0    0.089   0.089     3.525   57.500   57.500
LGA    P    22_A      P    22_A     2.091     0    0.608   0.765     4.219   57.857   54.694
LGA    G    23_A      G    23_A     2.483     0    0.313   0.313     4.593   58.452   58.452
LGA    V    24_A      V    24_A     2.486     0    0.615   0.607     6.153   75.357   53.061
LGA    A    25_A      A    25_A     1.469     0    0.184   0.194     3.761   70.000   64.667
LGA    F    26_A      F    26_A     3.733     0    0.109   1.254     5.355   65.833   41.082
LGA    R    27_A      R    27_A     3.204     0    0.087   1.249    11.882   52.024   26.450
LGA    A    28_A      A    28_A     2.060     0    0.303   0.346     2.081   72.976   71.333
LGA    P    29_A      P    29_A     3.370     0    0.660   0.613     5.722   42.976   42.313
LGA    S    30_A      S    30_A     1.620     0    0.016   0.033     2.190   81.548   77.302
LGA    I    31_A      I    31_A     1.392     0    0.284   1.296     4.693   73.214   63.929
LGA    H    32_A      H    32_A     1.480     0    0.674   1.423     7.390   65.119   47.857
LGA    G    33_A      G    33_A     3.710     0    0.064   0.064     3.710   61.548   61.548

# 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):    13.879         13.735                 15.083           28.023   23.331

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.59    37.121    34.595     0.520

LGA_LOCAL      RMSD:   2.593  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.422  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  13.879  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.091505 * X  +   0.982391 * Y  +  -0.162894 * Z  + -18.304268
  Y_new =  -0.989372 * X  +   0.071126 * Y  +  -0.126824 * Z  +  40.395054
  Z_new =  -0.113005 * X  +   0.172767 * Y  +   0.978459 * Z  +   2.212114 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.478571  0.113247  0.174769   [DEG:  -84.7159    6.4886   10.0135 ]
ZXZ: -0.909260  0.207938 -0.579243   [DEG:  -52.0968   11.9140  -33.1882 ]
 
# END of job
