
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.69     7.06
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.65    12.01
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.49    12.63
  LCS_AVERAGE:     39.35

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     8_D     L     8_F      3    3   20      0    3    3    3    3    3    4   14   15   17   17   18   19   19   21   23   24   25   26   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   20      3    3    5    6    6   10   13   14   15   17   17   18   19   20   23   23   24   25   26   26 
LCS_GDT     K    10_D     K    10_F      3    4   20      3    4    5    6    6    6    8   11   12   14   15   15   17   18   20   20   23   24   26   26 
LCS_GDT     L    11_D     L    11_F      3   12   20      3    4    5    6   10   11   13   14   15   17   17   18   19   20   23   23   24   25   26   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   18   20   21   23   23   24   25   26   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      7    8   10   11   11   11   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      7    8   10   11   11   11   13   14   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      5    8   11   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    7   10   11   11   11   13   14   15   17   17   18   20   20   21   23   24   25   26   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4   10   11   11   11   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     11   11   12   13   13   13   14   15   15   17   17   18   19   21   23   23   24   25   26   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     11   11   12   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     11   11   12   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     11   11   12   13   13   13   14   15   15   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   19   21   23   23   23   25   26   26 
LCS_GDT     R    32_D     R    32_F     12   13   22     11   11   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    7   12   13   13   13   14   15   15   16   17   19   20   21   23   23   24   25   26   26 
LCS_AVERAGE  LCS_A:  55.72  (  39.35   44.38   83.43 )

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     11     11     12     13     13     13     14     15     15     17     17     19     20     21     23     23     24     25     26     26 
GDT PERCENT_AT  42.31  42.31  46.15  50.00  50.00  50.00  53.85  57.69  57.69  65.38  65.38  73.08  76.92  80.77  88.46  88.46  92.31  96.15 100.00 100.00
GDT RMS_LOCAL    0.32   0.32   0.49   0.97   0.97   0.97   1.70   2.21   2.21   3.66   3.70   4.04   4.39   4.47   5.13   5.04   5.43   5.63   5.87   5.87
GDT RMS_ALL_AT  12.60  12.60  12.63  11.61  11.61  11.61  11.40  10.25  10.25   8.80   7.09   7.12   6.75   6.97   6.17   6.48   5.93   5.91   5.87   5.87

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    25.959     0    0.288   1.433    28.181    0.000    0.000
LGA    Q     9_D      Q     9_F    20.168     0    0.582   0.589    22.511    0.000    0.000
LGA    K    10_D      K    10_F    20.754     0    0.040   0.835    28.457    0.000    0.000
LGA    L    11_D      L    11_F    17.054     0    0.609   0.618    18.478    0.000    0.000
LGA    N    12_D      N    12_F    13.576     0    0.579   0.992    14.835    0.119    0.060
LGA    S    13_D      S    13_F    12.946     0    0.030   0.730    16.140    0.000    0.000
LGA    W    14_D      W    14_F    14.897     0    0.086   0.695    23.345    0.000    0.000
LGA    D    15_D      D    15_F    10.236     0    0.691   0.771    13.067    3.571    1.786
LGA    V    16_D      V    16_F     4.673     0    0.105   0.174     6.416   25.357   26.599
LGA    F    17_D      F    17_F     9.392     0    0.074   1.436    17.004    4.524    1.645
LGA    G    18_D      G    18_F     6.951     0    0.157   0.157     7.723   26.905   26.905
LGA    N    19_D      N    19_F     1.407     0    0.895   0.790     7.010   71.071   49.345
LGA    W    20_D      W    20_F     6.378     0    0.202   1.218    16.700   20.595    6.088
LGA    F    21_D      F    21_F     4.282     0    0.571   1.058    10.941   47.262   21.905
LGA    D    22_D      D    22_F     2.954     0    0.566   1.346     7.735   61.071   37.619
LGA    L    23_D      L    23_F     2.229     0    0.103   0.970     4.125   66.786   60.417
LGA    A    24_D      A    24_F     1.904     0    0.033   0.033     2.059   72.976   71.333
LGA    S    25_D      S    25_F     1.795     0    0.124   0.540     2.541   77.143   73.095
LGA    W    26_D      W    26_F     1.401     0    0.027   1.666     7.175   81.548   56.361
LGA    I    27_D      I    27_F     0.643     0    0.035   1.112     2.547   95.238   82.262
LGA    K    28_D      K    28_F     0.548     0    0.074   0.686     1.690   92.857   87.566
LGA    Y    29_D      Y    29_F     0.270     0    0.023   0.245     0.716   97.619   96.032
LGA    I    30_D      I    30_F     0.867     0    0.065   0.742     2.714   88.333   80.774
LGA    Q    31_D      Q    31_F     1.514     0    0.063   1.267     8.278   75.000   49.471
LGA    R    32_D      R    32_F     1.404     0    0.491   1.414     5.900   77.262   59.740
LGA    R    33_D      R    33_F     1.664     0    0.584   1.860     8.447   77.143   42.078

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.868          5.683                  7.351           44.707   35.811

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.21    59.615    55.123     0.649

LGA_LOCAL      RMSD:   2.209  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.249  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.868  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.948154 * X  +  -0.082287 * Y  +  -0.306974 * Z  + -106.873161
  Y_new =   0.148895 * X  +  -0.738322 * Y  +   0.657807 * Z  + -107.540741
  Z_new =  -0.280775 * X  +  -0.669409 * Y  +  -0.687791 * Z  +  45.956596 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.155764  0.284601 -2.369738   [DEG:    8.9246   16.3065 -135.7760 ]
ZXZ: -2.704969  2.329238 -2.744443   [DEG: -154.9833  133.4555 -157.2450 ]
 
# END of job
