
#######################################################
#                                                     #
#                        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:    25       9_A - 33_A        4.80     8.34
  LCS_AVERAGE:     68.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      17_A - 28_A        2.00     9.71
  LCS_AVERAGE:     27.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      17_A - 22_A        0.45    11.17
  LONGEST_CONTINUOUS_SEGMENT:     6      18_A - 23_A        0.94    10.29
  LCS_AVERAGE:     14.97

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   14      0    5    6    8    9   10   13   13   13   14   15   16   16   17   19   20   23   26   27   28 
LCS_GDT     R     2_A     R     2_A      5    7   14      3    5    6    8    9   10   13   13   13   14   15   16   16   16   19   20   20   21   22   22 
LCS_GDT     Q     3_A     Q     3_A      5    7   14      3    5    6    8    9   10   13   13   13   14   15   16   16   17   19   21   24   26   27   28 
LCS_GDT     S     4_A     S     4_A      5    7   15      3    5    6    8    9   10   13   13   13   14   15   16   16   18   21   21   24   26   27   28 
LCS_GDT     S     5_A     S     5_A      5    7   15      3    4    6    7    9   10   13   13   13   14   17   19   21   22   22   23   25   26   28   28 
LCS_GDT     A     6_A     A     6_A      5    7   15      3    4    5    8    9   10   12   12   13   16   18   19   21   22   23   26   26   26   28   28 
LCS_GDT     T     7_A     T     7_A      5    7   15      3    4    5    7    8   10   12   12   12   14   17   18   21   22   22   23   23   24   27   28 
LCS_GDT     S     8_A     S     8_A      5    5   23      3    4    5    5    6    7    8   10   13   16   18   19   21   22   22   24   25   26   28   28 
LCS_GDT     S     9_A     S     9_A      5    7   25      3    4    6    8    9   11   11   13   16   16   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     F    10_A     F    10_A      4    7   25      3    4    6    8    9   11   11   13   16   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    11_A     G    11_A      4    7   25      3    4    6    8    9   11   11   13   16   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    12_A     G    12_A      4    7   25      3    4    5    5    9   10   11   13   15   16   19   21   22   24   25   26   26   26   28   28 
LCS_GDT     L    13_A     L    13_A      3    9   25      4    4    5    8    9   11   11   13   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    14_A     G    14_A      3    9   25      4    4    5    8    9   11   12   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    15_A     G    15_A      5    9   25      3    3    5    7    9   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    16_A     G    16_A      5   10   25      3    3    5    7    9    9   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     S    17_A     S    17_A      6   12   25      3    6    6    9   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     V    18_A     V    18_A      6   12   25      5    6    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     R    19_A     R    19_A      6   12   25      5    6    7   10   11   12   13   15   17   17   19   21   22   23   25   26   26   26   28   28 
LCS_GDT     F    20_A     F    20_A      6   12   25      5    6    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    21_A     G    21_A      6   12   25      5    6    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     P    22_A     P    22_A      6   12   25      5    6    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    23_A     G    23_A      6   12   25      3    4    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     V    24_A     V    24_A      5   12   25      3    5    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     A    25_A     A    25_A      5   12   25      3    4    7   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     F    26_A     F    26_A      5   12   25      4    4    6   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     R    27_A     R    27_A      5   12   25      3    4    6   10   11   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     A    28_A     A    28_A      5   12   25      3    4    6    8    9   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     P    29_A     P    29_A      5    9   25      4    4    5    8    9   11   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     S    30_A     S    30_A      5    9   25      3    4    6    8    9   12   13   15   17   19   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     I    31_A     I    31_A      5    8   25      3    4    5    7    9   10   13   13   14   15   15   18   19   24   25   26   26   26   28   28 
LCS_GDT     H    32_A     H    32_A      5    8   25      3    3    6    8    9   12   13   14   16   16   20   21   22   24   25   26   26   26   28   28 
LCS_GDT     G    33_A     G    33_A      3    4   25      3    3    5    8    9   12   12   14   16   16   17   18   21   24   25   26   26   26   28   28 
LCS_AVERAGE  LCS_A:  37.16  (  14.97   27.64   68.87 )

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     10     11     12     13     15     17     19     20     21     22     24     25     26     26     26     28     28 
GDT PERCENT_AT  15.15  18.18  21.21  30.30  33.33  36.36  39.39  45.45  51.52  57.58  60.61  63.64  66.67  72.73  75.76  78.79  78.79  78.79  84.85  84.85
GDT RMS_LOCAL    0.13   0.45   1.03   1.43   1.62   2.09   2.32   2.68   3.14   3.78   3.91   4.03   4.17   4.71   4.80   5.08   5.08   5.08   5.68   5.68
GDT RMS_ALL_AT  10.78  11.17  10.23   9.95   9.90  11.93   9.60   9.43   9.08   8.32   8.16   8.10   8.19   8.25   8.34   8.16   8.16   8.16   7.89   7.89

# Checking swapping
#   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    15.032     0    0.311   1.155    15.332    0.000    0.000
LGA    R     2_A      R     2_A    17.921     0    0.324   1.548    26.774    0.000    0.000
LGA    Q     3_A      Q     3_A    12.980     0    0.081   0.415    15.767    0.000    0.000
LGA    S     4_A      S     4_A    13.643     0    0.042   0.591    14.844    0.000    0.000
LGA    S     5_A      S     5_A    12.456     0    0.532   0.786    14.571    0.000    0.000
LGA    A     6_A      A     6_A    12.286     0    0.112   0.157    14.874    0.000    0.000
LGA    T     7_A      T     7_A    18.637     0    0.603   0.552    21.646    0.000    0.000
LGA    S     8_A      S     8_A    17.492     0    0.659   0.849    20.821    0.000    0.000
LGA    S     9_A      S     9_A    10.326     0    0.706   0.910    12.879    0.000    0.794
LGA    F    10_A      F    10_A     9.588     0    0.696   1.153    14.353    1.786    0.779
LGA    G    11_A      G    11_A    10.911     0    0.265   0.265    12.098    0.000    0.000
LGA    G    12_A      G    12_A    11.216     0    0.162   0.162    11.216    0.119    0.119
LGA    L    13_A      L    13_A     9.971     0    0.586   1.045    11.095    0.476    0.298
LGA    G    14_A      G    14_A     7.224     0    0.616   0.616     8.033   10.476   10.476
LGA    G    15_A      G    15_A     3.752     0    0.514   0.514     5.113   37.500   37.500
LGA    G    16_A      G    16_A     3.311     0    0.308   0.308     3.311   51.786   51.786
LGA    S    17_A      S    17_A     1.533     0    0.243   0.672     3.696   72.976   69.444
LGA    V    18_A      V    18_A     1.988     0    0.020   1.048     3.402   77.143   67.551
LGA    R    19_A      R    19_A     2.304     0    0.069   1.485    14.520   64.762   30.693
LGA    F    20_A      F    20_A     1.374     0    0.111   0.270     2.796   71.071   81.255
LGA    G    21_A      G    21_A     2.050     0    0.187   0.187     2.251   68.810   68.810
LGA    P    22_A      P    22_A     1.216     0    0.628   0.678     3.756   71.905   73.537
LGA    G    23_A      G    23_A     2.068     0    0.575   0.575     3.825   61.667   61.667
LGA    V    24_A      V    24_A     2.632     0    0.079   1.171     4.532   62.857   56.803
LGA    A    25_A      A    25_A     3.279     0    0.099   0.101     3.913   51.786   50.095
LGA    F    26_A      F    26_A     3.174     0    0.173   1.185     4.537   53.571   58.528
LGA    R    27_A      R    27_A     2.984     0    0.044   1.057     5.671   59.286   40.216
LGA    A    28_A      A    28_A     2.293     0    0.097   0.134     4.099   77.619   69.524
LGA    P    29_A      P    29_A     5.306     0    0.641   0.605     8.729   32.976   21.837
LGA    S    30_A      S    30_A     4.173     0    0.117   0.711     8.233   24.643   35.476
LGA    I    31_A      I    31_A    10.822     0    0.630   0.854    15.511    1.190    0.595
LGA    H    32_A      H    32_A    10.121     0    0.088   1.154    10.816    0.000    0.143
LGA    G    33_A      G    33_A    11.153     0    0.451   0.451    13.537    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):     7.538          7.480                  8.909           28.921   26.907

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     15    2.68    43.182    39.858     0.539

LGA_LOCAL      RMSD:   2.681  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.433  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   7.538  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.815483 * X  +  -0.575864 * Y  +  -0.058045 * Z  +  14.837863
  Y_new =  -0.238195 * X  +  -0.425318 * Y  +   0.873137 * Z  +   0.915873
  Z_new =  -0.527495 * X  +  -0.698202 * Y  +  -0.484007 * Z  +  15.714988 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.284185  0.555649 -2.176957   [DEG:  -16.2826   31.8364 -124.7305 ]
ZXZ: -3.075212  2.076025 -2.494578   [DEG: -176.1967  118.9475 -142.9288 ]
 
# END of job
