
#######################################################
#                                                     #
#                        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      12_A - 32_A        4.85    18.74
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.57    19.38
  LCS_AVERAGE:     53.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      15_A - 26_A        1.88    20.36
  LCS_AVERAGE:     28.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      18_A - 26_A        0.84    20.20
  LCS_AVERAGE:     18.64

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    7   11      4    4    5    6    7    7    7    8    8    9    9    9    9   11   11   11   11   11   12   12 
LCS_GDT     R     2_A     R     2_A      5    7   11      4    4    5    6    7    7    7    8    8    9    9    9   10   11   11   11   11   11   12   12 
LCS_GDT     Q     3_A     Q     3_A      5    7   11      4    4    5    6    7    7    7    8    8    9    9    9   10   11   11   11   11   11   12   12 
LCS_GDT     S     4_A     S     4_A      5    7   11      4    4    5    6    7    7    7    8    8    9    9    9   10   11   11   11   11   11   12   12 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    6    7    7    7    8    8    9    9    9   10   11   11   11   11   11   12   14 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    5    6    7    7    7    8    8    9    9    9   10   11   13   13   13   13   13   14 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    6    7    7    7    8    9    9    9    9   10   11   13   13   13   14   14   15 
LCS_GDT     S     8_A     S     8_A      4    6   11      3    4    4    5    5    5    7    8    9    9   10   10   10   12   13   13   13   14   14   15 
LCS_GDT     S     9_A     S     9_A      3    5   11      3    3    3    4    4    6    6    8    9    9   10   10   10   12   13   13   13   14   14   15 
LCS_GDT     F    10_A     F    10_A      3    6   11      3    3    3    5    5    6    6    8    9    9   10   10   10   12   13   13   13   14   14   15 
LCS_GDT     G    11_A     G    11_A      5    6   16      3    3    5    5    5    6    6    8    9    9   10   10   10   13   13   15   16   18   19   20 
LCS_GDT     G    12_A     G    12_A      5    6   21      3    3    5    5    5    6    6    8    9   11   15   15   16   17   19   20   20   22   22   22 
LCS_GDT     L    13_A     L    13_A      5    6   21      3    3    5    5    5    6    8   10   13   14   15   17   18   18   20   20   21   22   22   22 
LCS_GDT     G    14_A     G    14_A      5    6   21      3    4    9   11   12   12   13   14   14   16   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     G    15_A     G    15_A      5   12   21      4    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     G    16_A     G    16_A      4   12   21      3    4    4    6    9    9   12   12   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     S    17_A     S    17_A      4   12   21      3    4    6    9   11   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     V    18_A     V    18_A      9   12   21      5    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     R    19_A     R    19_A      9   12   21      5    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     F    20_A     F    20_A      9   12   21      5    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     G    21_A     G    21_A      9   12   21      5    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     P    22_A     P    22_A      9   12   21      5    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     G    23_A     G    23_A      9   12   21      4    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     V    24_A     V    24_A      9   12   21      4    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     A    25_A     A    25_A      9   12   21      4    6   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     F    26_A     F    26_A      9   12   21      4    8   10   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     R    27_A     R    27_A      7   11   21      4    6    7   11   12   12   13   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     A    28_A     A    28_A      7   11   21      4    6    7    9   10   11   12   14   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     P    29_A     P    29_A      7   10   21      4    6    7    9   10   12   12   13   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     S    30_A     S    30_A      7   10   21      3    6    7    9   10   12   12   13   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     I    31_A     I    31_A      7   10   21      3    6    7    7    9   10   11   13   14   17   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     H    32_A     H    32_A      7   10   21      3    5    7    7    9   12   12   13   14   16   19   19   19   19   20   20   21   22   22   22 
LCS_GDT     G    33_A     G    33_A      4   10   21      3    3    6    7    8   10   11   11   11   11   11   13   13   13   19   20   21   22   22   22 
LCS_AVERAGE  LCS_A:  33.58  (  18.64   28.10   53.99 )

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      8     10     11     12     12     13     14     14     17     19     19     19     19     20     20     21     22     22     22 
GDT PERCENT_AT  15.15  24.24  30.30  33.33  36.36  36.36  39.39  42.42  42.42  51.52  57.58  57.58  57.58  57.58  60.61  60.61  63.64  66.67  66.67  66.67
GDT RMS_LOCAL    0.40   0.64   0.82   1.02   1.30   1.30   1.75   2.16   2.16   3.36   3.61   3.61   3.61   3.61   4.12   4.12   4.57   5.15   5.15   5.15
GDT RMS_ALL_AT  19.85  19.77  20.18  20.08  19.92  19.92  20.03  19.76  19.76  20.29  19.88  19.88  19.88  19.88  19.38  19.38  19.38  18.79  18.79  18.79

# 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    38.997     0    0.047   0.339    43.332    0.000    0.000
LGA    R     2_A      R     2_A    36.616     0    0.082   1.166    37.243    0.000    0.000
LGA    Q     3_A      Q     3_A    37.336     0    0.026   0.072    40.059    0.000    0.000
LGA    S     4_A      S     4_A    35.946     0    0.138   0.654    36.729    0.000    0.000
LGA    S     5_A      S     5_A    35.983     0    0.556   0.587    37.164    0.000    0.000
LGA    A     6_A      A     6_A    35.291     0    0.132   0.149    36.001    0.000    0.000
LGA    T     7_A      T     7_A    31.361     0    0.131   0.913    34.250    0.000    0.000
LGA    S     8_A      S     8_A    28.835     0    0.357   0.683    30.127    0.000    0.000
LGA    S     9_A      S     9_A    27.287     0    0.320   0.286    29.809    0.000    0.000
LGA    F    10_A      F    10_A    22.490     0    0.179   1.543    24.154    0.000    0.000
LGA    G    11_A      G    11_A    19.999     0    0.717   0.717    20.740    0.000    0.000
LGA    G    12_A      G    12_A    13.019     0    0.329   0.329    15.635    0.000    0.000
LGA    L    13_A      L    13_A     9.033     0    0.340   0.421    14.229    7.024    3.512
LGA    G    14_A      G    14_A     2.750     0    0.537   0.537     4.930   60.714   60.714
LGA    G    15_A      G    15_A     0.442     0    0.335   0.335     3.144   71.905   71.905
LGA    G    16_A      G    16_A     5.710     0    0.591   0.591     5.710   33.333   33.333
LGA    S    17_A      S    17_A     4.260     0    0.157   0.655     8.074   40.476   32.143
LGA    V    18_A      V    18_A     1.066     0    0.237   0.964     2.837   83.810   78.095
LGA    R    19_A      R    19_A     0.754     0    0.230   0.962     6.882   88.214   64.545
LGA    F    20_A      F    20_A     0.712     0    0.117   0.163     2.157   90.476   80.952
LGA    G    21_A      G    21_A     0.383     0    0.089   0.089     1.221   90.595   90.595
LGA    P    22_A      P    22_A     0.870     0    0.348   0.516     1.796   90.595   85.442
LGA    G    23_A      G    23_A     0.702     0    0.524   0.524     2.010   86.429   86.429
LGA    V    24_A      V    24_A     0.483     0    0.155   0.312     1.643   90.714   86.803
LGA    A    25_A      A    25_A     2.839     0    0.011   0.037     3.829   59.048   55.905
LGA    F    26_A      F    26_A     2.179     0    0.269   1.335     5.158   68.810   62.771
LGA    R    27_A      R    27_A     2.297     0    0.029   1.031     9.433   59.405   29.221
LGA    A    28_A      A    28_A     4.174     0    0.041   0.050     5.596   37.381   36.190
LGA    P    29_A      P    29_A     9.289     0    0.087   0.368    11.511    3.571    2.449
LGA    S    30_A      S    30_A     8.998     0    0.113   0.685    13.550    1.071    0.952
LGA    I    31_A      I    31_A    13.314     0    0.158   0.410    16.653    0.000    0.000
LGA    H    32_A      H    32_A    14.723     0    0.051   0.535    16.120    0.000    0.000
LGA    G    33_A      G    33_A    20.432     0    0.195   0.195    24.529    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):    15.201         15.070                 16.165           32.229   29.150

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.16    40.152    38.630     0.620

LGA_LOCAL      RMSD:   2.159  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.757  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  15.201  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.999598 * X  +   0.019840 * Y  +  -0.020234 * Z  +  -8.525965
  Y_new =  -0.002660 * X  +  -0.776545 * Y  +  -0.630056 * Z  +   0.143040
  Z_new =  -0.028213 * X  +  -0.629749 * Y  +   0.776286 * Z  +  -2.572707 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.138932  0.028217 -0.681554   [DEG: -179.8475    1.6167  -39.0501 ]
ZXZ: -0.032103  0.682044 -3.096822   [DEG:   -1.8394   39.0783 -177.4348 ]
 
# END of job
