
#######################################################
#                                                     #
#                        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       1_A - 21_A        4.75    15.43
  LONGEST_CONTINUOUS_SEGMENT:    21       2_A - 22_A        4.80    14.71
  LCS_AVERAGE:     62.63

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      11_A - 20_A        1.98    15.13
  LCS_AVERAGE:     23.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5      12_A - 16_A        0.97    15.31
  LONGEST_CONTINUOUS_SEGMENT:     5      13_A - 17_A        0.77    15.13
  LONGEST_CONTINUOUS_SEGMENT:     5      14_A - 18_A        0.92    15.03
  LONGEST_CONTINUOUS_SEGMENT:     5      27_A - 31_A        0.93    21.00
  LONGEST_CONTINUOUS_SEGMENT:     5      28_A - 32_A        0.91    20.51
  LCS_AVERAGE:     12.86

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    5   21      3    4    4    4    4    5    7    7    8    9   10   15   18   18   21   22   22   23   25   25 
LCS_GDT     R     2_A     R     2_A      4    5   21      3    4    4    4    4    5    7    7   12   13   14   18   20   20   21   22   22   23   25   25 
LCS_GDT     Q     3_A     Q     3_A      4    6   21      3    4    4    4    5    9   11   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     S     4_A     S     4_A      4    6   21      0    4    4    5    5   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     S     5_A     S     5_A      4    6   21      1    3    4    5    5   10   12   13   14   16   18   18   20   20   21   22   22   23   25   25 
LCS_GDT     A     6_A     A     6_A      4    6   21      3    3    4    5    7    9   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     T     7_A     T     7_A      4    6   21      3    3    4    5    7    9   11   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     S     8_A     S     8_A      3    6   21      3    3    4    5    5    6   11   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     S     9_A     S     9_A      4    6   21      3    4    4    7    7   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     F    10_A     F    10_A      4    9   21      3    4    5    7    7   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    11_A     G    11_A      4   10   21      3    4    5    7    9   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    12_A     G    12_A      5   10   21      3    4    6    8    9   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     L    13_A     L    13_A      5   10   21      3    5    6    8    9   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    14_A     G    14_A      5   10   21      3    5    6    8    9   10   11   12   13   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    15_A     G    15_A      5   10   21      3    5    6    8    9   10   12   13   14   16   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    16_A     G    16_A      5   10   21      3    5    6    8    9   11   12   14   16   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     S    17_A     S    17_A      5   10   21      3    5    6    8    9   10   12   13   16   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     V    18_A     V    18_A      5   10   21      3    5    6    8    9   10   12   13   14   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     R    19_A     R    19_A      4   10   21      3    3    4    7    9   11   12   14   16   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     F    20_A     F    20_A      4   10   21      3    5    5    8    9   11   12   14   16   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     G    21_A     G    21_A      4    7   21      3    3    4    6    9   11   12   14   16   17   18   19   20   20   21   22   22   23   25   25 
LCS_GDT     P    22_A     P    22_A      4    7   21      3    3    4    6    6    8   11   14   16   17   18   19   19   19   21   22   22   23   25   25 
LCS_GDT     G    23_A     G    23_A      4    7   20      3    3    4    6    9   11   12   14   16   17   18   18   18   19   19   21   22   23   25   25 
LCS_GDT     V    24_A     V    24_A      3    7   20      3    4    6    7    9   11   12   14   16   17   18   18   18   19   19   20   21   23   25   25 
LCS_GDT     A    25_A     A    25_A      3    8   20      3    4    6    7    8    9   12   14   16   17   18   18   18   19   19   20   21   23   25   25 
LCS_GDT     F    26_A     F    26_A      3    8   20      3    4    6    7    8    9   10   14   16   17   18   18   18   19   19   19   21   21   23   24 
LCS_GDT     R    27_A     R    27_A      5    8   20      3    3    5    6    7   11   12   14   16   17   18   18   18   19   19   19   21   21   23   24 
LCS_GDT     A    28_A     A    28_A      5    8   20      3    4    6    7    8   11   12   14   16   17   18   18   18   19   19   19   20   21   23   24 
LCS_GDT     P    29_A     P    29_A      5    8   20      3    4    6    7    9   11   12   14   16   17   18   18   18   19   19   19   20   21   23   24 
LCS_GDT     S    30_A     S    30_A      5    8   20      3    4    6    7    9   11   12   14   16   17   18   18   18   19   19   19   20   20   21   22 
LCS_GDT     I    31_A     I    31_A      5    8   20      3    4    5    6    8    8   10   13   16   17   18   18   18   19   19   19   20   20   20   21 
LCS_GDT     H    32_A     H    32_A      5    8   20      3    4    6    7    9   11   12   14   16   17   18   18   18   19   19   19   20   20   21   22 
LCS_GDT     G    33_A     G    33_A      3    4   20      3    3    4    6    9   11   12   14   16   17   18   18   18   19   19   19   20   20   20   22 
LCS_AVERAGE  LCS_A:  33.03  (  12.86   23.60   62.63 )

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      6      8      9     11     12     14     16     17     18     19     20     20     21     22     22     23     25     25 
GDT PERCENT_AT   9.09  15.15  18.18  24.24  27.27  33.33  36.36  42.42  48.48  51.52  54.55  57.58  60.61  60.61  63.64  66.67  66.67  69.70  75.76  75.76
GDT RMS_LOCAL    0.01   0.69   1.02   1.30   1.51   2.14   2.30   2.59   2.97   3.17   3.36   4.45   4.43   4.43   4.80   5.04   5.04   5.53   6.36   6.36
GDT RMS_ALL_AT  17.59  14.88  15.20  15.08  15.06  11.09  11.01  10.94  11.03  11.35  11.27  14.43  15.13  15.13  14.71  15.04  15.04  14.74  14.26  14.26

# 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    16.852     0    0.044   1.390    19.193    0.000    0.000
LGA    R     2_A      R     2_A    11.371     0    0.076   1.110    13.100    0.000    0.043
LGA    Q     3_A      Q     3_A    10.878     0    0.632   0.992    17.472    1.310    0.582
LGA    S     4_A      S     4_A    11.308     0    0.650   0.797    13.599    0.000    0.000
LGA    S     5_A      S     5_A    17.134     0    0.259   0.323    18.872    0.000    0.000
LGA    A     6_A      A     6_A    15.103     0    0.671   0.617    15.405    0.000    0.000
LGA    T     7_A      T     7_A    16.303     0    0.068   1.048    19.148    0.000    0.000
LGA    S     8_A      S     8_A    17.771     0    0.632   0.848    20.217    0.000    0.000
LGA    S     9_A      S     9_A    19.129     0    0.049   0.654    19.768    0.000    0.000
LGA    F    10_A      F    10_A    16.191     0    0.667   1.119    18.024    0.000    0.000
LGA    G    11_A      G    11_A    22.054     0    0.708   0.708    22.054    0.000    0.000
LGA    G    12_A      G    12_A    19.978     0    0.353   0.353    20.692    0.000    0.000
LGA    L    13_A      L    13_A    15.999     0    0.116   0.209    20.315    0.000    0.000
LGA    G    14_A      G    14_A    11.328     0    0.094   0.094    13.481    2.857    2.857
LGA    G    15_A      G    15_A     8.484     0    0.314   0.314     9.747    5.833    5.833
LGA    G    16_A      G    16_A     3.287     0    0.459   0.459     4.570   55.000   55.000
LGA    S    17_A      S    17_A     5.963     0    0.532   0.745     9.389   20.357   14.286
LGA    V    18_A      V    18_A     5.605     0    0.693   0.599     8.246   35.000   26.327
LGA    R    19_A      R    19_A     2.768     0    0.078   1.293     8.840   55.595   35.758
LGA    F    20_A      F    20_A     1.218     0    0.585   1.441     9.746   71.905   39.091
LGA    G    21_A      G    21_A     2.490     0    0.137   0.137     2.928   65.119   65.119
LGA    P    22_A      P    22_A     5.053     0    0.646   0.645     7.087   30.476   23.810
LGA    G    23_A      G    23_A     0.963     0    0.345   0.345     3.471   71.548   71.548
LGA    V    24_A      V    24_A     2.431     0    0.593   1.023     6.244   69.048   50.136
LGA    A    25_A      A    25_A     3.612     0    0.608   0.560     6.281   52.381   45.333
LGA    F    26_A      F    26_A     3.633     0    0.426   1.230     4.970   55.595   44.502
LGA    R    27_A      R    27_A     2.562     0    0.658   1.206    14.459   63.214   28.571
LGA    A    28_A      A    28_A     3.324     0    0.185   0.234     6.041   59.286   50.857
LGA    P    29_A      P    29_A     2.808     0    0.514   0.593     6.765   67.143   47.755
LGA    S    30_A      S    30_A     1.951     0    0.034   0.597     3.494   67.262   61.508
LGA    I    31_A      I    31_A     5.454     0    0.600   0.525    12.480   37.500   19.464
LGA    H    32_A      H    32_A     1.150     0    0.009   1.157     6.931   65.357   50.381
LGA    G    33_A      G    33_A     1.957     0    0.543   0.543     5.235   54.405   54.405

# 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):     9.708          9.560                 10.475           30.491   24.035

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.59    37.121    34.914     0.521

LGA_LOCAL      RMSD:   2.587  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.938  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.708  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.881605 * X  +   0.439589 * Y  +  -0.171854 * Z  + -17.334028
  Y_new =   0.464446 * X  +  -0.743137 * Y  +   0.481702 * Z  +   6.254042
  Z_new =   0.084040 * X  +  -0.504488 * Y  +  -0.859319 * Z  +   2.887350 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.484871 -0.084139 -2.610728   [DEG:   27.7811   -4.8208 -149.5837 ]
ZXZ: -2.798905  2.604733  2.976524   [DEG: -160.3654  149.2402  170.5422 ]
 
# END of job
