
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        1.99     1.99
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.99     1.99
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36      57_A - 98_A        0.97     2.91
  LCS_AVERAGE:     49.21

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A     23   61   61     16   26   38   44   49   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     23   61   61     15   26   38   44   49   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     23   61   61     16   26   39   44   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     23   61   61     16   26   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     23   61   61      7   28   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     23   61   61     16   26   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     23   61   61     16   26   39   45   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     23   61   61     16   29   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     23   61   61      5   22   36   44   48   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     23   61   61     15   25   34   43   48   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     23   61   61     15   26   36   44   48   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     23   61   61      3    3   15   29   41   47   56   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     23   61   61      3    3   26   34   41   50   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A      3   61   61      3    3    4    4   37   45   48   52   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A      3   61   61      3    3    4    8   18   50   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     36   61   61      5   30   37   45   50   54   56   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     36   61   61     13   30   37   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     36   61   61     16   30   37   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     36   61   61     22   30   37   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     36   61   61     23   30   38   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     36   61   61     22   30   38   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     36   61   61     16   30   38   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     36   61   61      3   28   38   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     36   61   61      5   10   20   34   43   51   55   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     36   61   61      3    3    6   45   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     36   61   61      3    9   38   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     36   61   61      3   24   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     36   61   61     23   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     36   61   61     20   30   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     36   61   61      3   28   39   47   50   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  83.07  (  49.21  100.00  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     30     39     47     50     54     57     60     60     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  37.70  49.18  63.93  77.05  81.97  88.52  93.44  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.49   0.90   1.17   1.28   1.51   1.70   1.89   1.89   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99
GDT RMS_ALL_AT   2.81   3.03   2.09   2.24   2.26   2.06   2.00   2.00   2.00   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     2.715     0    0.532   0.529     4.237   55.357   51.714
LGA    T    33_A      T    33_A     2.298     0    0.079   0.276     2.645   66.786   68.367
LGA    M    34_A      M    34_A     2.124     0    0.057   0.641     2.590   70.952   66.905
LGA    A    35_A      A    35_A     1.708     0    0.097   0.104     1.883   75.000   74.571
LGA    D    36_A      D    36_A     1.312     0    0.116   0.200     2.370   83.690   77.321
LGA    L    37_A      L    37_A     1.627     0    0.039   0.117     2.688   79.286   71.071
LGA    K    38_A      K    38_A     1.221     0    0.130   0.934     2.732   88.333   77.090
LGA    M    39_A      M    39_A     0.163     0    0.028   1.063     4.817   97.619   80.476
LGA    Q    40_A      Q    40_A     0.916     0    0.049   1.161     5.055   90.476   72.963
LGA    A    41_A      A    41_A     0.659     0    0.049   0.050     0.781   92.857   92.381
LGA    V    42_A      V    42_A     0.132     0    0.062   0.123     0.629  100.000   98.639
LGA    K    43_A      K    43_A     0.718     0    0.009   0.121     2.637   92.857   81.005
LGA    E    44_A      E    44_A     1.041     0    0.159   0.741     3.429   81.548   69.947
LGA    I    45_A      I    45_A     0.429     0    0.049   0.117     0.897   95.238   95.238
LGA    C    46_A      C    46_A     0.711     0    0.082   0.143     1.335   90.595   90.556
LGA    Y    47_A      Y    47_A     1.327     0    0.030   1.210    10.052   83.690   45.357
LGA    E    48_A      E    48_A     0.954     0    0.008   0.180     1.042   88.214   87.460
LGA    V    49_A      V    49_A     0.664     0    0.032   0.054     1.391   85.952   86.599
LGA    A    50_A      A    50_A     2.541     0    0.112   0.122     3.388   59.286   58.857
LGA    L    51_A      L    51_A     3.178     0    0.018   0.156     3.682   50.119   50.060
LGA    A    52_A      A    52_A     2.585     0    0.687   0.662     3.698   53.690   57.524
LGA    D    53_A      D    53_A     4.164     0    0.526   0.853     9.073   43.452   26.429
LGA    F    54_A      F    54_A     3.818     0    0.290   1.206     9.647   38.690   24.069
LGA    R    55_A      R    55_A     5.447     0    0.088   1.060    10.676   30.119   12.900
LGA    H    56_A      H    56_A     3.608     0    0.637   1.046    10.393   45.595   21.952
LGA    G    57_A      G    57_A     3.600     0    0.579   0.579     3.600   55.833   55.833
LGA    R    58_A      R    58_A     2.910     0    0.047   1.286     9.125   57.262   40.433
LGA    A    59_A      A    59_A     2.954     0    0.030   0.029     3.393   57.262   55.810
LGA    E    60_A      E    60_A     2.625     0    0.027   0.418     5.041   62.976   47.566
LGA    I    61_A      I    61_A     1.543     0    0.020   0.119     2.019   77.381   80.536
LGA    E    62_A      E    62_A     1.255     0    0.013   0.170     2.700   81.429   73.122
LGA    A    63_A      A    63_A     1.437     0    0.000   0.014     1.904   81.548   79.810
LGA    L    64_A      L    64_A     1.296     0    0.178   0.433     1.912   81.429   80.417
LGA    A    65_A      A    65_A     0.687     0    0.020   0.022     0.988   95.238   94.286
LGA    A    66_A      A    66_A     0.442     0    0.060   0.066     0.769   95.238   94.286
LGA    L    67_A      L    67_A     0.425     0    0.014   0.788     2.698   95.238   87.560
LGA    K    68_A      K    68_A     1.108     0    0.030   0.877     1.393   85.952   85.450
LGA    M    69_A      M    69_A     0.601     0    0.047   0.586     1.894   90.476   89.524
LGA    R    70_A      R    70_A     0.441     0    0.124   0.620     5.249   92.976   67.359
LGA    E    71_A      E    71_A     1.252     0    0.055   1.073     3.803   79.405   69.947
LGA    L    72_A      L    72_A     1.497     0    0.019   0.156     1.855   77.143   79.286
LGA    C    73_A      C    73_A     1.600     0    0.069   0.253     1.978   75.000   75.714
LGA    R    74_A      R    74_A     2.148     0    0.261   0.933     7.075   59.524   48.398
LGA    T    75_A      T    75_A     2.503     0    0.228   1.025     3.490   62.857   60.476
LGA    Y    76_A      Y    76_A     2.679     0    0.548   1.618    10.320   57.262   32.738
LGA    G    83_A      G    83_A     4.219     0    0.303   0.303     4.450   45.357   45.357
LGA    D    84_A      D    84_A     2.900     0    0.248   0.334     3.812   61.190   56.548
LGA    A    85_A      A    85_A     1.954     0    0.021   0.023     2.605   77.381   73.333
LGA    W    86_A      W    86_A     1.194     0    0.060   1.176     9.407   83.690   44.116
LGA    R    87_A      R    87_A     1.035     0    0.038   1.006     2.220   83.690   77.662
LGA    A    88_A      A    88_A     0.936     0    0.129   0.143     1.248   88.214   86.857
LGA    V    89_A      V    89_A     0.613     0    0.052   0.104     0.841   90.476   91.837
LGA    A    90_A      A    90_A     0.715     0    0.036   0.039     0.952   90.476   90.476
LGA    R    91_A      R    91_A     0.704     0    0.015   1.246     7.883   90.476   61.732
LGA    D    92_A      D    92_A     0.511     0    0.065   0.191     1.079   95.238   91.726
LGA    V    93_A      V    93_A     0.795     0    0.014   0.107     0.889   90.476   90.476
LGA    W    94_A      W    94_A     1.098     0    0.013   0.336     2.068   85.952   79.694
LGA    D    95_A      D    95_A     0.793     0    0.214   0.472     1.647   86.071   87.143
LGA    T    96_A      T    96_A     1.029     0    0.108   1.154     2.978   88.214   80.612
LGA    V    97_A      V    97_A     1.072     0    0.569   1.341     2.922   77.619   76.939
LGA    G    98_A      G    98_A     1.298     0    0.073   0.073     1.416   85.952   85.952

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     1.992          1.940                  3.175           76.743   69.811

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     60    1.89    81.148    89.258     3.017

LGA_LOCAL      RMSD:   1.889  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.999  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.992  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.786850 * X  +  -0.102117 * Y  +  -0.608637 * Z  + -18.016714
  Y_new =  -0.555675 * X  +  -0.311841 * Y  +   0.770701 * Z  +  64.231522
  Z_new =  -0.268500 * X  +   0.944631 * Y  +   0.188628 * Z  +  -7.617669 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.526716  0.271835  1.373704   [DEG: -144.7702   15.5750   78.7075 ]
ZXZ: -2.473153  1.381032 -0.276934   [DEG: -141.7012   79.1273  -15.8672 ]
 
# END of job
