
#######################################################
#                                                     #
#                        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:    24       5_A - 28_A        4.89     8.56
  LONGEST_CONTINUOUS_SEGMENT:    24       6_A - 29_A        4.92     8.47
  LCS_AVERAGE:     66.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      13_A - 21_A        2.00    10.21
  LCS_AVERAGE:     23.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      18_A - 23_A        0.92    14.87
  LCS_AVERAGE:     13.04

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    8   13      4    4    4    6    7    8    9   11   13   14   16   16   17   18   20   22   24   26   28   28 
LCS_GDT     R     2_A     R     2_A      4    8   13      4    4    4    6    7    8    9   11   13   14   16   16   17   18   20   22   24   26   28   28 
LCS_GDT     Q     3_A     Q     3_A      4    8   13      4    4    4    6    7    8    9   11   13   14   16   16   17   18   20   22   23   26   28   28 
LCS_GDT     S     4_A     S     4_A      5    8   21      4    4    5    6    7    8    9   11   13   14   16   16   17   18   20   22   24   26   28   28 
LCS_GDT     S     5_A     S     5_A      5    8   24      3    4    5    5    7    8    9   11   13   14   16   19   21   23   25   26   26   27   28   28 
LCS_GDT     A     6_A     A     6_A      5    8   24      3    4    5    5    7    8    9   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     T     7_A     T     7_A      5    8   24      3    4    5    5    7    9   10   13   15   17   18   20   22   23   25   26   26   27   28   28 
LCS_GDT     S     8_A     S     8_A      5    8   24      3    4    5    5    7    9   10   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     S     9_A     S     9_A      3    8   24      3    3    4    5    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     F    10_A     F    10_A      3    6   24      3    3    4    6    8   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    11_A     G    11_A      3    6   24      3    3    4    5    6    8    9   11   14   16   17   19   21   23   25   26   26   27   28   28 
LCS_GDT     G    12_A     G    12_A      3    6   24      3    3    4    6    8   10   11   13   14   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     L    13_A     L    13_A      5    9   24      3    4    5    6    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    14_A     G    14_A      5    9   24      3    4    5    6    7   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    15_A     G    15_A      5    9   24      3    4    5    6    8   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    16_A     G    16_A      5    9   24      3    4    5    6    8   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     S    17_A     S    17_A      5    9   24      3    4    6    6    7   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     V    18_A     V    18_A      6    9   24      4    5    6    7    8   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     R    19_A     R    19_A      6    9   24      4    5    6    7    7    9   11   13   14   16   17   19   21   23   25   26   26   27   28   28 
LCS_GDT     F    20_A     F    20_A      6    9   24      3    5    6    7    8   10   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    21_A     G    21_A      6    9   24      4    5    6    7    8   10   11   13   14   16   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     P    22_A     P    22_A      6    8   24      4    5    6    7    8   10   11   13   13   16   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     G    23_A     G    23_A      6    8   24      3    5    6    7    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     V    24_A     V    24_A      5    8   24      3    3    6    7    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     A    25_A     A    25_A      3    8   24      3    3    4    5    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     F    26_A     F    26_A      3    6   24      3    3    4    6    7    9   11   13   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     R    27_A     R    27_A      3    7   24      3    3    4    6    7    8   10   11   15   17   19   20   22   23   25   26   26   27   28   28 
LCS_GDT     A    28_A     A    28_A      3    7   24      3    3    4    5    7    8    9   11   12   13   15   19   22   23   25   26   26   27   28   28 
LCS_GDT     P    29_A     P    29_A      3    7   24      3    3    4    5    7    7   10   11   12   13   16   19   22   23   25   26   26   27   28   28 
LCS_GDT     S    30_A     S    30_A      3    7   15      3    3    4    5    7    8   10   11   12   13   14   15   16   19   23   25   26   27   28   28 
LCS_GDT     I    31_A     I    31_A      3    7   15      3    3    3    5    7    8   10   11   12   13   14   15   16   18   19   20   21   23   24   27 
LCS_GDT     H    32_A     H    32_A      3    7   15      3    3    3    5    7    8   10   11   12   13   14   15   16   19   23   25   26   27   28   28 
LCS_GDT     G    33_A     G    33_A      3    7   15      3    3    3    4    7    7    9   10   12   12   14   15   19   23   25   26   26   27   28   28 
LCS_AVERAGE  LCS_A:  34.28  (  13.04   23.69   66.12 )

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      7      8     10     11     13     15     17     19     20     22     23     25     26     26     27     28     28 
GDT PERCENT_AT  12.12  15.15  18.18  21.21  24.24  30.30  33.33  39.39  45.45  51.52  57.58  60.61  66.67  69.70  75.76  78.79  78.79  81.82  84.85  84.85
GDT RMS_LOCAL    0.14   0.55   0.92   1.13   1.95   2.24   2.40   2.74   3.35   3.64   4.10   4.18   4.70   4.67   5.06   5.36   5.36   5.89   5.98   5.98
GDT RMS_ALL_AT  14.88  16.07  14.87  15.88   9.45   9.43   9.69   9.40   9.12   8.97   9.36   9.17   8.48   8.87   8.37   8.04   8.04   8.11   8.02   8.02

# 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    17.708     0    0.126   0.353    18.203    0.000    0.000
LGA    R     2_A      R     2_A    16.469     0    0.026   1.376    17.209    0.000    0.000
LGA    Q     3_A      Q     3_A    15.280     0    0.179   1.194    18.138    0.000    0.000
LGA    S     4_A      S     4_A    14.600     0    0.655   0.838    17.987    0.000    0.000
LGA    S     5_A      S     5_A    11.623     0    0.559   0.868    12.436    0.000    0.000
LGA    A     6_A      A     6_A     7.625     0    0.104   0.125    10.341    3.214    6.000
LGA    T     7_A      T     7_A     8.902     0    0.174   0.490    12.116    7.024    4.014
LGA    S     8_A      S     8_A     6.596     0    0.563   0.524     7.747   13.810   13.095
LGA    S     9_A      S     9_A     4.045     0    0.687   0.620     5.442   52.619   45.635
LGA    F    10_A      F    10_A     2.675     0    0.691   1.357    10.064   45.238   24.848
LGA    G    11_A      G    11_A     5.438     0    0.185   0.185     5.438   40.952   40.952
LGA    G    12_A      G    12_A     2.660     0    0.262   0.262     4.025   52.619   52.619
LGA    L    13_A      L    13_A     3.468     0    0.694   1.278    10.184   59.286   32.560
LGA    G    14_A      G    14_A     1.890     0    0.318   0.318     2.328   72.976   72.976
LGA    G    15_A      G    15_A     2.587     0    0.664   0.664     3.290   61.190   61.190
LGA    G    16_A      G    16_A     2.436     0    0.668   0.668     3.947   59.405   59.405
LGA    S    17_A      S    17_A     3.061     0    0.229   0.246     7.384   65.357   48.810
LGA    V    18_A      V    18_A     1.661     0    0.145   1.160     5.466   75.119   57.347
LGA    R    19_A      R    19_A     3.526     0    0.165   1.647    15.120   50.357   20.303
LGA    F    20_A      F    20_A     1.658     0    0.076   1.428    11.543   75.476   33.983
LGA    G    21_A      G    21_A     1.281     0    0.070   0.070     3.052   71.429   71.429
LGA    P    22_A      P    22_A     3.096     0    0.117   0.476     6.268   46.429   54.354
LGA    G    23_A      G    23_A     6.312     0    0.617   0.617     9.882   14.881   14.881
LGA    V    24_A      V    24_A    10.482     0    0.617   0.545    13.441    0.714    0.408
LGA    A    25_A      A    25_A    12.730     0    0.156   0.203    13.353    0.000    0.000
LGA    F    26_A      F    26_A    12.421     0    0.234   1.237    13.795    0.000    0.000
LGA    R    27_A      R    27_A    11.614     0    0.663   1.187    18.429    2.143    0.779
LGA    A    28_A      A    28_A     8.555     0    0.205   0.248    11.061    1.190    1.048
LGA    P    29_A      P    29_A     8.966     0    0.101   0.356     9.936    2.143    7.211
LGA    S    30_A      S    30_A    12.316     0    0.530   0.812    15.949    0.000    0.000
LGA    I    31_A      I    31_A    16.850     0    0.066   1.215    20.460    0.000    0.000
LGA    H    32_A      H    32_A    13.105     0    0.124   1.342    16.251    0.119    0.048
LGA    G    33_A      G    33_A     8.917     0    0.079   0.079    10.530    2.143    2.143

# 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):     7.757          7.654                  8.742           26.540   22.001

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     13    2.74    38.636    35.296     0.458

LGA_LOCAL      RMSD:   2.737  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.400  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   7.757  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.210586 * X  +   0.977568 * Y  +  -0.003839 * Z  + -38.419327
  Y_new =  -0.913384 * X  +  -0.195357 * Y  +   0.357164 * Z  +  40.209003
  Z_new =   0.348402 * X  +   0.078720 * Y  +   0.934034 * Z  + -96.770889 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.797393 -0.355866  0.084081   [DEG: -102.9830  -20.3896    4.8175 ]
ZXZ: -3.130845  0.365252  1.348582   [DEG: -179.3842   20.9274   77.2681 ]
 
# END of job
