
#######################################################
#                                                     #
#                        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:    22       1_A - 22_A        4.80    16.00
  LONGEST_CONTINUOUS_SEGMENT:    22       2_A - 23_A        4.99    15.08
  LONGEST_CONTINUOUS_SEGMENT:    22      12_A - 33_A        4.56    11.02
  LCS_AVERAGE:     66.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      13_A - 24_A        1.68    12.32
  LCS_AVERAGE:     29.57

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       5_A - 9_A         0.92    19.99
  LONGEST_CONTINUOUS_SEGMENT:     5      15_A - 19_A        0.70    15.78
  LONGEST_CONTINUOUS_SEGMENT:     5      20_A - 24_A        0.96    11.46
  LONGEST_CONTINUOUS_SEGMENT:     5      26_A - 30_A        0.63    20.62
  LCS_AVERAGE:     13.41

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    9   22      3    4    5    8   10   11   13   14   15   16   17   19   20   20   21   22   22   22   24   24 
LCS_GDT     R     2_A     R     2_A      4    9   22      3    4    5    8   10   11   13   14   15   16   17   19   20   20   21   22   22   22   24   24 
LCS_GDT     Q     3_A     Q     3_A      4    9   22      3    4    5    8   10   12   13   14   15   16   18   19   20   20   21   22   22   22   24   24 
LCS_GDT     S     4_A     S     4_A      4    9   22      3    4    4    6    9   11   13   14   15   16   18   19   20   20   21   22   22   22   24   24 
LCS_GDT     S     5_A     S     5_A      5   10   22      3    4    5    8   10   12   13   14   15   16   18   19   20   20   21   22   22   22   24   24 
LCS_GDT     A     6_A     A     6_A      5   10   22      3    4    5    8   10   12   13   14   15   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     T     7_A     T     7_A      5   10   22      3    3    5    8   10   12   13   14   15   16   18   19   20   20   21   22   22   24   24   25 
LCS_GDT     S     8_A     S     8_A      5   10   22      1    4    5    8   10   12   13   14   15   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     S     9_A     S     9_A      5   10   22      3    4    5    8   10   12   13   14   15   16   18   19   20   20   22   23   24   24   25   26 
LCS_GDT     F    10_A     F    10_A      3   10   22      3    3    5    6    9   12   13   14   15   16   18   19   20   20   23   23   24   24   25   26 
LCS_GDT     G    11_A     G    11_A      3   10   22      3    3    4    6    9   12   13   14   15   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     G    12_A     G    12_A      3   10   22      3    4    4    7   10   12   13   14   15   16   18   19   20   20   23   23   24   24   25   26 
LCS_GDT     L    13_A     L    13_A      3   12   22      3    4    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    14_A     G    14_A      3   12   22      3    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    15_A     G    15_A      5   12   22      4    5    6    9   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    16_A     G    16_A      5   12   22      3    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     S    17_A     S    17_A      5   12   22      3    4    6    9   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     V    18_A     V    18_A      5   12   22      4    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     R    19_A     R    19_A      5   12   22      4    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     F    20_A     F    20_A      5   12   22      4    5    6   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    21_A     G    21_A      5   12   22      4    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     P    22_A     P    22_A      5   12   22      4    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    23_A     G    23_A      5   12   22      3    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     V    24_A     V    24_A      5   12   22      4    6    8   10   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     A    25_A     A    25_A      4    8   22      3    4    5    6    7   10   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     F    26_A     F    26_A      5    8   22      4    5    6    7    7   10   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     R    27_A     R    27_A      5    8   22      4    5    5    6    7   10   13   13   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     A    28_A     A    28_A      5    7   22      4    5    5    6    7   10   13   13   14   15   18   21   21   21   23   23   24   24   25   26 
LCS_GDT     P    29_A     P    29_A      5    7   22      4    5    5    6    6    7   11   13   14   16   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     S    30_A     S    30_A      5    7   22      3    5    5    7    7   10   13   13   14   16   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     I    31_A     I    31_A      4    7   22      3    3    4    7    7    9   13   13   14   16   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     H    32_A     H    32_A      4    5   22      3    3    4    5    5    9   13   13   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_GDT     G    33_A     G    33_A      3    5   22      3    3    6    9   12   13   13   14   15   17   19   21   21   21   23   23   24   24   25   26 
LCS_AVERAGE  LCS_A:  36.55  (  13.41   29.57   66.67 )

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      6      8     10     12     13     13     14     15     17     19     21     21     21     23     23     24     24     25     26 
GDT PERCENT_AT  12.12  18.18  24.24  30.30  36.36  39.39  39.39  42.42  45.45  51.52  57.58  63.64  63.64  63.64  69.70  69.70  72.73  72.73  75.76  78.79
GDT RMS_LOCAL    0.14   0.72   1.03   1.25   1.61   1.78   1.78   2.13   2.38   2.99   3.70   4.10   4.10   4.10   4.87   4.87   5.21   5.21   5.57   5.99
GDT RMS_ALL_AT  13.15  12.09  12.64  12.42  12.34  12.48  12.48  12.23  12.09  11.90  11.52  11.27  11.27  11.27  10.83  10.83  10.60  10.60  10.60  10.39

# 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    29.281     0    0.268   1.100    35.078    0.000    0.000
LGA    R     2_A      R     2_A    22.911     0    0.156   1.244    25.406    0.000    0.000
LGA    Q     3_A      Q     3_A    20.103     0    0.189   1.173    20.518    0.000    0.000
LGA    S     4_A      S     4_A    20.362     0    0.111   0.568    21.164    0.000    0.000
LGA    S     5_A      S     5_A    22.466     0    0.549   0.646    24.209    0.000    0.000
LGA    A     6_A      A     6_A    18.906     0    0.081   0.118    19.731    0.000    0.000
LGA    T     7_A      T     7_A    21.852     0    0.581   1.334    26.172    0.000    0.000
LGA    S     8_A      S     8_A    18.386     0    0.651   0.865    21.291    0.000    0.000
LGA    S     9_A      S     9_A    12.961     0    0.726   0.761    15.031    0.000    0.000
LGA    F    10_A      F    10_A    10.108     0    0.622   1.390    14.275    1.190    0.693
LGA    G    11_A      G    11_A    12.846     0    0.068   0.068    12.846    0.000    0.000
LGA    G    12_A      G    12_A     9.382     0    0.286   0.286    10.601    6.190    6.190
LGA    L    13_A      L    13_A     2.504     0    0.158   1.404     5.086   46.310   41.905
LGA    G    14_A      G    14_A     1.258     0    0.233   0.233     1.553   79.286   79.286
LGA    G    15_A      G    15_A     3.140     0    0.105   0.105     3.140   63.333   63.333
LGA    G    16_A      G    16_A     1.381     0    0.176   0.176     3.123   73.571   73.571
LGA    S    17_A      S    17_A     1.996     0    0.194   0.684     6.546   71.429   56.032
LGA    V    18_A      V    18_A     2.087     0    0.049   1.065     6.433   79.643   56.939
LGA    R    19_A      R    19_A     1.476     0    0.145   0.251    11.333   73.452   36.494
LGA    F    20_A      F    20_A     1.647     0    0.094   1.489    10.517   79.643   36.970
LGA    G    21_A      G    21_A     1.168     0    0.161   0.161     1.718   81.548   81.548
LGA    P    22_A      P    22_A     1.247     0    0.100   0.107     2.136   81.548   76.667
LGA    G    23_A      G    23_A     1.024     0    0.297   0.297     2.644   82.262   82.262
LGA    V    24_A      V    24_A     1.244     0    0.083   1.067     5.345   71.905   56.327
LGA    A    25_A      A    25_A     4.874     0    0.248   0.291     7.502   42.262   35.238
LGA    F    26_A      F    26_A     4.494     0    0.132   1.257    10.594   22.976   14.892
LGA    R    27_A      R    27_A     5.986     0    0.150   0.746    10.448   22.857   15.108
LGA    A    28_A      A    28_A     9.518     0    0.060   0.076    11.863    5.000    4.000
LGA    P    29_A      P    29_A     9.100     0    0.658   0.614    11.854    1.071    0.612
LGA    S    30_A      S    30_A     9.681     0    0.043   0.582    11.493    2.024    1.349
LGA    I    31_A      I    31_A     9.329     0    0.627   1.226    10.913    1.548    1.250
LGA    H    32_A      H    32_A     7.280     0    0.097   1.391    12.996   24.643   10.143
LGA    G    33_A      G    33_A     2.180     0    0.295   0.295     4.361   57.857   57.857

# 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):     9.513          9.287                 10.698           32.471   26.929

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.13    40.152    39.317     0.629

LGA_LOCAL      RMSD:   2.127  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.225  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.513  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.839937 * X  +   0.298113 * Y  +  -0.453469 * Z  +  50.140087
  Y_new =   0.425045 * X  +  -0.880909 * Y  +   0.208173 * Z  +  14.577028
  Z_new =  -0.337406 * X  +  -0.367597 * Y  +  -0.866620 * Z  + -58.170422 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.468471  0.344160 -2.740423   [DEG:   26.8414   19.7189 -157.0146 ]
ZXZ: -2.001165  2.619184 -2.398992   [DEG: -114.6583  150.0682 -137.4521 ]
 
# END of job
