
#######################################################
#                                                     #
#                        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   29 (  227),  selected   29 , name one
# Molecule2: number of CA atoms  151 ( 1194),  selected   29 , 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:    26     100_A - 125_A       4.90     5.70
  LCS_AVERAGE:     16.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      97_A - 112_A       1.84    15.34
  LCS_AVERAGE:      9.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      97_A - 111_A       0.67    16.14
  LCS_AVERAGE:      7.70

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   29
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     L    97_A     L    97_A     15   16   20      9   13   15   15   15   15   15   15   16   16   16   17   17   19   22   27   28   29   29   29 
LCS_GDT     V    98_A     V    98_A     15   16   20      9   14   15   15   15   15   15   15   17   19   20   23   25   25   26   27   28   29   29   29 
LCS_GDT     S    99_A     S    99_A     15   16   20      9   14   15   15   15   15   15   15   16   16   16   17   20   23   23   27   28   29   29   29 
LCS_GDT     T   100_A     T   100_A     15   16   26      9   14   15   15   15   15   15   15   16   16   16   17   17   19   22   27   28   29   29   29 
LCS_GDT     F   101_A     F   101_A     15   16   26      9   14   15   15   15   15   15   15   16   16   20   23   25   25   26   27   28   29   29   29 
LCS_GDT     T   102_A     T   102_A     15   16   26      9   14   15   15   15   15   15   17   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     Q   103_A     Q   103_A     15   16   26      9   14   15   15   15   15   15   15   16   16   16   19   25   25   26   27   28   29   29   29 
LCS_GDT     Q   104_A     Q   104_A     15   16   26      9   14   15   15   15   15   15   15   16   16   20   23   25   25   26   27   28   29   29   29 
LCS_GDT     F   105_A     F   105_A     15   16   26      9   14   15   15   15   15   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     V   106_A     V   106_A     15   16   26      9   14   15   15   15   15   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     D   107_A     D   107_A     15   16   26      9   14   15   15   15   15   15   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     V   108_A     V   108_A     15   16   26      9   14   15   15   15   15   15   16   17   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     I   109_A     I   109_A     15   16   26      9   14   15   15   15   15   15   15   17   20   21   22   22   24   26   27   28   29   29   29 
LCS_GDT     R   110_A     R   110_A     15   16   26      9   14   15   15   15   15   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     G   111_A     G   111_A     15   16   26      9   14   15   15   15   15   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     D   112_A     D   112_A     10   16   26      6   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     P   113_A     P   113_A     10   13   26      6   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     Q   114_A     Q   114_A     10   13   26      6   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     A   115_A     A   115_A     10   13   26      6   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     V   116_A     V   116_A     10   13   26      6   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     A   117_A     A   117_A     10   13   26      5   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     E   118_A     E   118_A     10   13   26      5   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     H   119_A     H   119_A     10   13   26      4   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     L   120_A     L   120_A     10   13   26      4   10   11   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     N   121_A     N   121_A      8   13   26      4    7    8   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     I   122_A     I   122_A      4   13   26      4    7    8   11   13   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     S   123_A     S   123_A      4   13   26      3    4    5    9   11   14   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     L   124_A     L   124_A      3    7   26      3    4    4    5    6    8   11   16   16   20   21   23   25   25   26   27   28   29   29   29 
LCS_GDT     E   125_A     E   125_A      3    7   26      0    3    3    6    9   13   17   18   19   20   21   23   25   25   26   27   28   29   29   29 
LCS_AVERAGE  LCS_A:  11.31  (   7.70    9.43   16.81 )

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      9     14     15     15     15     15     17     18     19     20     21     23     25     25     26     27     28     29     29     29 
GDT PERCENT_AT   5.96   9.27   9.93   9.93   9.93   9.93  11.26  11.92  12.58  13.25  13.91  15.23  16.56  16.56  17.22  17.88  18.54  19.21  19.21  19.21
GDT RMS_LOCAL    0.24   0.60   0.67   0.67   0.67   0.67   2.38   2.55   2.81   2.95   3.10   3.89   4.33   4.33   4.47   4.80   5.43   5.47   5.47   5.47
GDT RMS_ALL_AT  15.88  16.08  16.14  16.14  16.14  16.14   7.23   7.07   6.70   7.12   7.32   6.01   5.74   5.74   5.79   5.63   5.48   5.47   5.47   5.47

# Checking swapping
#   possible swapping detected:  F   101_A      F   101_A
#   possible swapping detected:  E   118_A      E   118_A
#   possible swapping detected:  E   125_A      E   125_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    97_A      L    97_A    17.745     0    0.064   0.181    19.849    0.000    0.000
LGA    V    98_A      V    98_A    11.162     0    0.032   1.157    13.654    0.119    0.476
LGA    S    99_A      S    99_A    14.746     0    0.141   0.661    18.371    0.000    0.000
LGA    T   100_A      T   100_A    15.879     0    0.041   0.975    19.871    0.000    0.000
LGA    F   101_A      F   101_A    10.286     0    0.055   1.400    12.221    5.119    4.372
LGA    T   102_A      T   102_A     6.228     0    0.067   0.194    10.244   13.929   10.816
LGA    Q   103_A      Q   103_A    10.104     0    0.054   1.274    16.870    2.857    1.270
LGA    Q   104_A      Q   104_A     9.034     0    0.092   0.994    16.713    8.333    3.704
LGA    F   105_A      F   105_A     3.376     0    0.025   1.333     8.418   53.452   37.316
LGA    V   106_A      V   106_A     3.008     0    0.032   0.127     7.118   61.071   41.293
LGA    D   107_A      D   107_A     4.437     0    0.031   1.191    10.874   45.119   24.167
LGA    V   108_A      V   108_A     5.614     0    0.043   0.222     9.252   25.476   16.599
LGA    I   109_A      I   109_A     5.656     0    0.042   1.315     9.714   26.786   17.202
LGA    R   110_A      R   110_A     3.053     0    0.035   1.345    13.580   59.405   27.013
LGA    G   111_A      G   111_A     3.813     0    0.275   0.275     3.813   50.357   50.357
LGA    D   112_A      D   112_A     1.444     0    0.079   0.195     2.553   81.548   73.214
LGA    P   113_A      P   113_A     0.993     0    0.103   0.328     1.888   83.810   81.565
LGA    Q   114_A      Q   114_A     2.750     0    0.101   1.030     8.188   61.071   41.852
LGA    A   115_A      A   115_A     2.451     0    0.023   0.032     2.804   68.810   66.476
LGA    V   116_A      V   116_A     0.476     0    0.054   1.046     2.998   90.595   82.381
LGA    A   117_A      A   117_A     2.275     0    0.048   0.073     2.905   64.881   63.333
LGA    E   118_A      E   118_A     2.682     0    0.039   0.731     6.998   65.000   42.222
LGA    H   119_A      H   119_A     1.032     0    0.015   1.111     4.448   88.333   70.286
LGA    L   120_A      L   120_A     1.061     0    0.692   1.007     4.114   72.857   72.262
LGA    N   121_A      N   121_A     1.440     0    0.466   1.072     3.896   67.738   65.595
LGA    I   122_A      I   122_A     1.462     0    0.189   1.123     4.974   77.262   65.060
LGA    S   123_A      S   123_A     2.488     0    0.292   0.575     5.076   50.238   51.349
LGA    L   124_A      L   124_A     5.772     0    0.656   0.713    11.261   34.762   18.810
LGA    E   125_A      E   125_A     3.371     0    0.491   0.906     4.473   52.500   48.307

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       29     116    116  100.00     227    227  100.00               151
SUMMARY(RMSD_GDC):     5.472          5.148                  6.837            8.685    7.134

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   29  151    4.0     18    2.55    12.252    11.464     0.679

LGA_LOCAL      RMSD:   2.552  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.074  Number of assigned atoms:   29 
Std_ASGN_ATOMS RMSD:   5.472  Standard rmsd on all 29 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.045508 * X  +  -0.963966 * Y  +  -0.262104 * Z  +   9.379351
  Y_new =  -0.107824 * X  +   0.256104 * Y  +  -0.960617 * Z  +  -8.710696
  Z_new =   0.993128 * X  +   0.071977 * Y  +  -0.092284 * Z  + -38.087242 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.171420 -1.453494  2.479197   [DEG:  -67.1174  -83.2791  142.0475 ]
ZXZ: -0.266366  1.663211  1.498448   [DEG:  -15.2617   95.2950   85.8548 ]
 
# END of job
