
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , 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:    32       4_A - 35_A        4.87     6.18
  LCS_AVERAGE:     90.37

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       2_A - 16_A        1.80    11.94
  LCS_AVERAGE:     30.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       6_A - 15_A        0.94    12.17
  LCS_AVERAGE:     17.71

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     S     1_A     S     1_A      6   12   26      3    4    6    8    8   11   13   14   18   19   21   23   24   25   27   29   32   33   34   34 
LCS_GDT     D     2_A     D     2_A      6   15   26      3    4    6    9   13   16   16   16   18   20   22   23   24   25   26   28   32   33   34   34 
LCS_GDT     E     3_A     E     3_A      7   15   31      3    5    8   13   14   16   16   17   18   20   22   25   26   29   29   29   32   33   34   34 
LCS_GDT     M     4_A     M     4_A      9   15   32      3    7    9   13   14   16   16   18   20   23   24   26   28   29   29   30   32   33   34   34 
LCS_GDT     W     5_A     W     5_A      9   15   32      3    5    9   13   14   16   16   18   20   21   24   25   28   29   29   30   32   33   34   34 
LCS_GDT     F     6_A     F     6_A     10   15   32      3    8   10   13   14   16   16   18   20   23   25   26   28   29   29   30   32   33   34   34 
LCS_GDT     C     7_A     C     7_A     10   15   32      6    8   10   13   14   16   18   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     E     8_A     E     8_A     10   15   32      6    8   10   13   14   16   18   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     T     9_A     T     9_A     10   15   32      6    8   10   13   14   16   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     L    10_A     L    10_A     10   15   32      6    8   10   13   14   16   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     R    11_A     R    11_A     10   15   32      6    8   10   13   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     R    12_A     R    12_A     10   15   32      6    8   10   13   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     L    13_A     L    13_A     10   15   32      3    8   10   13   14   16   16   19   23   25   26   26   27   29   29   30   32   33   34   34 
LCS_GDT     L    14_A     L    14_A     10   15   32      3    6   10   13   14   16   16   17   18   22   24   25   27   27   29   29   31   33   34   34 
LCS_GDT     C    15_A     C    15_A     10   15   32      3    5   10   13   14   16   16   17   18   21   23   25   27   27   29   29   32   33   34   34 
LCS_GDT     P    16_A     P    16_A      5   15   32      3    4    8   11   13   16   16   17   20   22   24   25   27   28   29   30   32   33   34   34 
LCS_GDT     K    17_A     K    17_A      3    6   32      3    5    7   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     S    18_A     S    18_A      4    6   32      3    4    6   10   13   15   18   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     C    19_A     C    19_A      4    6   32      3    4    7   10   13   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     S    20_A     S    20_A      4    8   32      3    4    6   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     I    21_A     I    21_A      4    8   32      3    4    4    9   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     E    22_A     E    22_A      3    8   32      3    3    5   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     G    23_A     G    23_A      3    8   32      3    3    3    4    8   13   18   19   22   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     G    24_A     G    24_A      4    8   32      0    4    7   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     C    25_A     C    25_A      4    8   32      4    5    7   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     P    26_A     P    26_A      4    8   32      4    5    6   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     E    27_A     E    27_A      4    8   32      4    4    6   11   14   17   18   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     V    28_A     V    28_A      5    7   32      4    5    8   10   13   15   18   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     C    29_A     C    29_A      5    7   32      4    5    8   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     S    30_A     S    30_A      5    7   32      4    5    8   11   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     H    31_A     H    31_A      5    7   32      4    5    8   10   14   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     M    32_A     M    32_A      5    7   32      3    5    5    6   13   15   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     C    33_A     C    33_A      3    7   32      4    4    8   10   13   17   19   21   24   25   26   26   28   29   29   30   32   33   34   34 
LCS_GDT     P    34_A     P    34_A      3    7   32      3    5    7   11   14   17   19   21   24   25   26   26   28   29   29   30   31   32   34   34 
LCS_GDT     L    35_A     L    35_A      3    6   32      0    3    7   13   14   17   19   21   24   25   26   26   28   29   29   30   31   32   33   34 
LCS_AVERAGE  LCS_A:  46.20  (  17.71   30.53   90.37 )

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      6      8     10     13     14     17     19     21     24     25     26     26     28     29     29     30     32     33     34     34 
GDT PERCENT_AT  17.14  22.86  28.57  37.14  40.00  48.57  54.29  60.00  68.57  71.43  74.29  74.29  80.00  82.86  82.86  85.71  91.43  94.29  97.14  97.14
GDT RMS_LOCAL    0.25   0.58   0.94   1.36   1.44   2.13   2.73   2.88   3.16   3.24   3.35   3.35   4.05   4.15   4.15   4.37   5.32   5.49   5.61   5.47
GDT RMS_ALL_AT  10.74  10.97  12.17  12.13  12.21   8.15   7.25   7.10   6.84   6.89   6.99   6.99   6.24   6.22   6.22   6.14   5.87   5.89   5.79   5.80

# Checking swapping
#   possible swapping detected:  F     6_A      F     6_A
#   possible swapping detected:  E    27_A      E    27_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A    19.509     0    0.359   0.814    24.065    0.000    0.000
LGA    D     2_A      D     2_A    17.684     0    0.176   1.419    20.661    0.000    0.000
LGA    E     3_A      E     3_A    13.953     0    0.117   1.031    18.692    0.119    0.053
LGA    M     4_A      M     4_A    10.520     0    0.070   0.530    14.317    0.714    0.357
LGA    W     5_A      W     5_A    11.368     0    0.048   0.945    17.966    1.310    0.374
LGA    F     6_A      F     6_A     8.669     0    0.039   0.296    10.152   10.714    4.069
LGA    C     7_A      C     7_A     4.260     0    0.086   0.229     6.071   44.286   47.540
LGA    E     8_A      E     8_A     4.654     0    0.078   0.890     8.681   40.476   21.376
LGA    T     9_A      T     9_A     4.328     0    0.032   0.267     7.770   49.643   33.741
LGA    L    10_A      L    10_A     3.454     0    0.020   0.076     7.663   52.024   34.940
LGA    R    11_A      R    11_A     2.433     0    0.099   1.253     5.987   58.690   42.857
LGA    R    12_A      R    12_A     2.000     0    0.105   1.086     9.317   63.095   36.926
LGA    L    13_A      L    13_A     4.941     0    0.072   1.259     8.215   26.667   19.702
LGA    L    14_A      L    14_A     9.484     0    0.122   1.443    14.485    2.976    1.488
LGA    C    15_A      C    15_A    10.029     0    0.554   0.919    10.763    1.429    0.952
LGA    P    16_A      P    16_A     8.720     0    0.631   0.683    10.752    6.190    3.605
LGA    K    17_A      K    17_A     2.583     0    0.626   0.988     7.735   54.048   48.519
LGA    S    18_A      S    18_A     5.620     0    0.682   0.792     9.555   35.000   24.603
LGA    C    19_A      C    19_A     3.127     0    0.064   0.833     4.416   62.619   55.159
LGA    S    20_A      S    20_A     2.855     0    0.044   0.686     4.564   55.595   48.492
LGA    I    21_A      I    21_A     2.431     0    0.552   1.005     5.639   53.452   48.214
LGA    E    22_A      E    22_A     2.618     0    0.647   1.165     7.168   50.833   39.312
LGA    G    23_A      G    23_A     4.823     0    0.494   0.494     4.823   42.024   42.024
LGA    G    24_A      G    24_A     2.028     0    0.405   0.405     2.159   64.762   64.762
LGA    C    25_A      C    25_A     2.345     0    0.178   0.668     3.546   62.857   59.921
LGA    P    26_A      P    26_A     1.685     0    0.511   0.596     1.762   72.857   72.857
LGA    E    27_A      E    27_A     3.473     0    0.105   1.286    10.610   63.571   31.481
LGA    V    28_A      V    28_A     4.451     0    0.700   0.929     8.524   52.262   35.170
LGA    C    29_A      C    29_A     2.957     0    0.184   0.920     4.327   59.524   55.397
LGA    S    30_A      S    30_A     2.869     0    0.073   0.629     4.921   67.500   56.429
LGA    H    31_A      H    31_A     2.416     0    0.410   1.400     6.025   61.190   48.619
LGA    M    32_A      M    32_A     3.587     0    0.125   0.314     7.344   46.905   35.417
LGA    C    33_A      C    33_A     2.173     0    0.302   0.345     3.263   70.952   65.159
LGA    P    34_A      P    34_A     1.815     0    0.623   0.532     5.233   61.667   62.177
LGA    L    35_A      L    35_A     3.095     0    0.296   1.285     6.999   52.500   41.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     5.753          5.563                  6.610           41.384   33.817

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     21    2.88    51.429    48.435     0.705

LGA_LOCAL      RMSD:   2.878  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.100  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   5.753  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.457615 * X  +  -0.644901 * Y  +   0.612120 * Z  +  -3.118995
  Y_new =   0.786441 * X  +  -0.027633 * Y  +  -0.617047 * Z  +   1.180381
  Z_new =   0.414849 * X  +   0.763766 * Y  +   0.494531 * Z  + -11.126423 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.043806 -0.427777  0.996187   [DEG:   59.8057  -24.5098   57.0773 ]
ZXZ:  0.781390  1.053501  0.497578   [DEG:   44.7703   60.3612   28.5091 ]
 
# END of job
