
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       5_B - 47_B        2.76     2.76
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       5_B - 43_B        1.93     3.17
  LCS_AVERAGE:     85.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_B - 34_B        0.93     3.18
  LONGEST_CONTINUOUS_SEGMENT:    30       6_B - 35_B        0.98     3.35
  LCS_AVERAGE:     58.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     5_B     S     5_B     30   39   43      5   20   28   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     30   39   43     20   26   28   32   34   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     30   39   43     16   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     30   39   43     20   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     30   39   43     14   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     30   39   43      9   26   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     30   39   43      7   15   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     30   39   43      7   13   21   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     30   39   43      7   16   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     17   39   43      7   13   29   32   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     17   39   43      7   13   16   25   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     17   39   43      7   13   16   19   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     17   39   43      7   13   16   25   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     17   39   43      7   13   16   20   35   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     17   39   43      3   12   16   19   25   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     16   39   43      5   10   15   19   23   38   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     12   39   43      4    7   11   16   19   23   33   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   24   43      4    5    9   12   16   20   24   37   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   21   43      4    5    7   11   14   17   21   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   14   43      3    3    3    3    5    7    8   12   15   24   32   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3   28   29   30   34   38   40   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  81.34  (  58.41   85.61  100.00 )

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     20     26     29     32     35     38     38     40     42     42     42     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  46.51  60.47  67.44  74.42  81.40  88.37  88.37  93.02  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.44   0.91   1.05   1.40   1.68   1.68   2.10   2.52   2.52   2.52   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76
GDT RMS_ALL_AT   3.33   3.25   3.32   3.37   3.62   3.40   3.40   2.96   2.80   2.80   2.80   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     1.510     0    0.613   0.917     4.634   77.143   63.889
LGA    L     6_B      L     6_B     0.613     0    0.047   0.866     3.456   90.476   79.226
LGA    E     7_B      E     7_B     0.740     0    0.061   0.765     2.954   88.214   80.899
LGA    T     8_B      T     8_B     1.094     0    0.035   1.218     2.828   83.690   76.871
LGA    K     9_B      K     9_B     0.981     0    0.018   0.108     1.095   88.214   87.460
LGA    K    10_B      K    10_B     0.914     0    0.043   0.933     3.963   88.214   81.376
LGA    A    11_B      A    11_B     1.123     0    0.027   0.040     1.286   83.690   83.238
LGA    Y    12_B      Y    12_B     1.321     0    0.021   0.047     1.999   79.286   75.714
LGA    A    13_B      A    13_B     1.267     0    0.050   0.061     1.365   81.429   81.429
LGA    A    14_B      A    14_B     1.311     0    0.088   0.097     1.605   79.286   79.714
LGA    R    15_B      R    15_B     1.579     0    0.032   0.815     3.024   75.000   72.338
LGA    T    16_B      T    16_B     1.780     0    0.025   0.035     2.232   75.000   72.925
LGA    R    17_B      R    17_B     0.679     0    0.073   1.065     2.942   88.214   77.922
LGA    R    18_B      R    18_B     1.626     0    0.029   0.641     2.108   75.000   73.723
LGA    S    19_B      S    19_B     2.208     0    0.042   0.633     3.433   70.833   65.079
LGA    N    20_B      N    20_B     1.620     0    0.067   0.490     1.769   77.143   78.214
LGA    Y    21_B      Y    21_B     0.850     0    0.054   0.167     2.269   85.952   82.381
LGA    A    22_B      A    22_B     1.473     0    0.035   0.033     1.688   81.429   79.714
LGA    A    23_B      A    23_B     1.673     0    0.044   0.050     1.812   77.143   76.286
LGA    S    24_B      S    24_B     1.186     0    0.079   0.718     1.905   83.690   81.508
LGA    L    25_B      L    25_B     0.826     0    0.026   0.082     0.983   90.476   90.476
LGA    R    26_B      R    26_B     1.074     0    0.018   0.979     3.347   85.952   75.714
LGA    L    27_B      L    27_B     1.037     0    0.063   0.195     2.202   85.952   80.536
LGA    E    28_B      E    28_B     0.433     0    0.060   0.526     1.396   97.619   92.751
LGA    G    29_B      G    29_B     0.657     0    0.037   0.037     0.740   90.476   90.476
LGA    F    30_B      F    30_B     0.901     0    0.074   0.109     1.165   85.952   90.563
LGA    K    31_B      K    31_B     1.512     0    0.056   0.627     5.738   79.286   60.529
LGA    V    32_B      V    32_B     0.864     0    0.045   1.225     3.512   85.952   78.639
LGA    T    33_B      T    33_B     1.384     0    0.066   1.036     3.614   81.548   74.830
LGA    F    34_B      F    34_B     2.263     0    0.016   1.400     3.674   66.786   62.987
LGA    A    35_B      A    35_B     1.857     0    0.029   0.028     2.082   70.833   72.952
LGA    D    36_B      D    36_B     1.476     0    0.010   0.366     2.136   72.976   78.393
LGA    G    37_B      G    37_B     2.639     0    0.021   0.021     3.447   55.476   55.476
LGA    E    38_B      E    38_B     3.389     0    0.035   0.183     5.131   50.119   43.810
LGA    R    39_B      R    39_B     3.204     0    0.120   1.159     4.722   48.333   50.087
LGA    K    40_B      K    40_B     3.281     0    0.053   1.242     5.538   48.333   50.423
LGA    M    41_B      M    41_B     3.487     0    0.031   0.802     4.240   46.667   44.286
LGA    P    42_B      P    42_B     3.835     0    0.074   0.081     4.768   38.810   42.653
LGA    T    43_B      T    43_B     5.451     0    0.008   0.054     5.934   26.310   24.218
LGA    R    44_B      R    44_B     6.968     0    0.604   0.940    14.131   11.667    5.281
LGA    E    45_B      E    45_B     7.614     0    0.476   1.261    10.632    8.571    6.561
LGA    E    46_B      E    46_B     9.691     0    0.595   1.420    14.317    2.381    1.058
LGA    V    47_B      V    47_B     4.906     0    0.397   1.359     6.575   20.833   33.469

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     2.765          2.750                  3.408           69.311   66.420

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     40    2.10    81.977    85.785     1.820

LGA_LOCAL      RMSD:   2.098  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.959  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.765  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.648211 * X  +  -0.386719 * Y  +   0.655951 * Z  +  26.176085
  Y_new =  -0.709506 * X  +   0.006004 * Y  +   0.704674 * Z  + -33.132145
  Z_new =  -0.276449 * X  +  -0.922178 * Y  +  -0.270487 * Z  +  18.425953 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.830513  0.280097 -1.856107   [DEG:  -47.5849   16.0484 -106.3471 ]
ZXZ:  2.391989  1.844695 -2.850339   [DEG:  137.0509  105.6933 -163.3124 ]
 
# END of job
