
#######################################################
#                                                     #
#                        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        2.87     2.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.86     3.15
  LCS_AVERAGE:     69.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.99     3.75
  LCS_AVERAGE:     53.76

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     29   33   43      5   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   33   43     22   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   33   43     21   26   28   29   30   31   34   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   33   43     23   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   33   43     17   26   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   33   43      8   25   28   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   33   43      7   10   12   25   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     13   33   43      7   10   12   16   20   30   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     13   33   43      7   10   12   16   20   30   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     13   33   43      7   10   12   19   27   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     13   33   43      7   10   12   16   20   28   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     13   23   43      7   10   12   16   20   22   30   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     13   23   43      7   10   12   16   20   24   31   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     13   23   43      6   10   12   16   20   25   31   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     13   23   43      3   10   12   16   20   28   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     13   23   43      4   10   12   16   20   28   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     12   23   43      4    8   11   14   20   22   34   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     11   22   43      4    7   11   12   17   22   29   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   21   43      4    6    7   11   13   19   29   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   14   43      3    3    3    5    6    7   10   12   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0   21   27   29   30   31   35   39   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  74.45  (  53.76   69.61  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     23     26     28     29     30     31     35     39     42     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  53.49  60.47  65.12  67.44  69.77  72.09  81.40  90.70  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.38   0.55   0.82   1.06   1.31   2.10   2.47   2.73   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87
GDT RMS_ALL_AT   4.55   4.49   4.31   3.69   3.51   3.35   3.01   2.93   2.90   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87   2.87

# Checking swapping
#   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     2.231     0    0.613   0.910     4.345   70.833   61.746
LGA    L     6_B      L     6_B     1.067     0    0.041   0.858     2.868   85.952   77.500
LGA    E     7_B      E     7_B     0.637     0    0.062   1.109     4.083   90.595   80.635
LGA    T     8_B      T     8_B     1.664     0    0.044   1.176     3.139   75.000   68.503
LGA    K     9_B      K     9_B     1.189     0    0.014   0.103     2.322   85.952   77.831
LGA    K    10_B      K    10_B     0.782     0    0.049   0.938     4.265   85.952   78.571
LGA    A    11_B      A    11_B     1.660     0    0.025   0.039     1.968   75.000   74.571
LGA    Y    12_B      Y    12_B     1.899     0    0.042   0.073     3.181   72.857   64.405
LGA    A    13_B      A    13_B     1.210     0    0.010   0.013     1.398   81.429   83.238
LGA    A    14_B      A    14_B     1.762     0    0.095   0.109     2.345   70.952   69.714
LGA    R    15_B      R    15_B     2.607     0    0.044   0.750     4.468   59.048   50.996
LGA    T    16_B      T    16_B     2.405     0    0.033   0.094     3.110   68.810   64.966
LGA    R    17_B      R    17_B     1.068     0    0.076   1.098     3.394   77.143   77.056
LGA    R    18_B      R    18_B     2.622     0    0.023   0.861     7.921   59.048   39.307
LGA    S    19_B      S    19_B     3.131     0    0.046   0.642     4.219   55.357   50.317
LGA    N    20_B      N    20_B     1.868     0    0.078   0.494     2.213   75.119   72.976
LGA    Y    21_B      Y    21_B     0.878     0    0.066   0.193     4.072   83.690   67.778
LGA    A    22_B      A    22_B     2.059     0    0.068   0.066     2.497   66.786   66.381
LGA    A    23_B      A    23_B     2.163     0    0.067   0.073     2.410   68.810   68.000
LGA    S    24_B      S    24_B     1.130     0    0.093   0.716     1.908   83.810   83.095
LGA    L    25_B      L    25_B     0.856     0    0.028   0.080     1.432   90.476   87.083
LGA    R    26_B      R    26_B     1.449     0    0.016   1.102     4.263   81.429   68.225
LGA    L    27_B      L    27_B     1.337     0    0.076   0.209     2.685   81.429   76.250
LGA    E    28_B      E    28_B     0.649     0    0.052   0.517     1.869   90.476   87.513
LGA    G    29_B      G    29_B     0.878     0    0.042   0.042     0.951   90.476   90.476
LGA    F    30_B      F    30_B     0.991     0    0.066   0.136     1.325   85.952   90.563
LGA    K    31_B      K    31_B     1.662     0    0.140   0.647     5.613   79.286   60.529
LGA    V    32_B      V    32_B     1.191     0    0.064   0.285     2.698   79.286   75.510
LGA    T    33_B      T    33_B     1.861     0    0.071   1.070     4.544   73.214   64.830
LGA    F    34_B      F    34_B     3.613     0    0.028   1.397     4.266   46.786   47.100
LGA    A    35_B      A    35_B     3.902     0    0.023   0.030     4.028   41.786   42.095
LGA    D    36_B      D    36_B     2.571     0    0.012   0.105     2.999   57.143   68.274
LGA    G    37_B      G    37_B     3.635     0    0.031   0.031     4.734   40.476   40.476
LGA    E    38_B      E    38_B     5.220     0    0.044   0.263     6.605   26.310   22.698
LGA    R    39_B      R    39_B     4.917     0    0.125   1.009     6.281   31.429   30.823
LGA    K    40_B      K    40_B     4.896     0    0.094   0.809     5.317   31.429   32.857
LGA    M    41_B      M    41_B     3.818     0    0.036   0.270     4.538   40.238   41.964
LGA    P    42_B      P    42_B     3.976     0    0.060   0.066     4.075   40.238   41.565
LGA    T    43_B      T    43_B     4.503     0    0.005   0.029     5.026   35.714   33.129
LGA    R    44_B      R    44_B     4.962     0    0.605   0.900    10.060   31.429   17.532
LGA    E    45_B      E    45_B     5.283     0    0.474   1.421    10.044   27.500   17.672
LGA    E    46_B      E    46_B     7.102     0    0.592   1.438    12.410   18.929    8.571
LGA    V    47_B      V    47_B     3.108     0    0.404   1.363     5.806   45.119   40.340

# 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):     2.874          2.815                  3.501           64.156   59.620

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     39    2.47    79.651    79.029     1.516

LGA_LOCAL      RMSD:   2.473  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.927  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.874  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.565827 * X  +  -0.196207 * Y  +  -0.800838 * Z  +  23.563494
  Y_new =  -0.809405 * X  +  -0.052968 * Y  +   0.584857 * Z  + -30.833469
  Z_new =  -0.157172 * X  +   0.979131 * Y  +  -0.128840 * Z  +  20.838507 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.180895  0.157826  1.701631   [DEG: -124.9561    9.0428   97.4963 ]
ZXZ: -2.201574  1.699996 -0.159164   [DEG: -126.1409   97.4026   -9.1194 ]
 
# END of job
