
#######################################################
#                                                     #
#                        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   56 (  450),  selected   49 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   49 , 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:    28      33_A - 60_A        4.71    28.77
  LONGEST_CONTINUOUS_SEGMENT:    28      54_A - 81_A        4.27    30.00
  LCS_AVERAGE:     38.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      58_A - 81_A        1.49    31.87
  LCS_AVERAGE:     31.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      59_A - 81_A        0.58    31.81
  LCS_AVERAGE:     29.14

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     Q    33_A     Q    33_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     L    34_A     L    34_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     L    35_A     L    35_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     S    36_A     S    36_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     G    37_A     G    37_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     I    38_A     I    38_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     V    39_A     V    39_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     Q    40_A     Q    40_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     Q    41_A     Q    41_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     Q    42_A     Q    42_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     N    43_A     N    43_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     N    44_A     N    44_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     L    45_A     L    45_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     L    46_A     L    46_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     R    47_A     R    47_A     22   23   28     14   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     A    48_A     A    48_A     22   23   28     13   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     I    49_A     I    49_A     22   23   28     11   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     E    50_A     E    50_A     22   23   28     11   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     A    51_A     A    51_A     22   23   28     13   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   28 
LCS_GDT     Q    52_A     Q    52_A     22   23   28     12   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   29 
LCS_GDT     Q    53_A     Q    53_A     22   23   28     15   21   22   22   22   22   22   22   22   24   24   25   25   25   26   26   27   28   28   29 
LCS_GDT     H    54_A     H    54_A     22   23   28      9   16   22   22   22   22   22   22   22   24   24   25   25   25   26   26   28   28   28   29 
LCS_GDT     L    55_A     L    55_A      4   23   28      3    4    4    5   10   12   15   18   21   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     L    56_A     L    56_A      4    4   28      3    4    4    5    7    7   10   15   19   21   24   25   25   26   27   27   28   28   28   29 
LCS_GDT     Q    57_A     Q    57_A      4    4   28      3    3    5    7   11   16   17   22   22   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     L    58_A     L    58_A      3   24   28      3    4    4    4    7    7   13   18   23   24   24   24   26   26   27   27   28   28   28   29 
LCS_GDT     T    59_A     T    59_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   28 
LCS_GDT     V    60_A     V    60_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     W    61_A     W    61_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     G    62_A     G    62_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     I    63_A     I    63_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     K    64_A     K    64_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     Q    65_A     Q    65_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     L    66_A     L    66_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     Q    67_A     Q    67_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     A    68_A     A    68_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     R    69_A     R    69_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     I    70_A     I    70_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     L    71_A     L    71_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     A    72_A     A    72_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     V    73_A     V    73_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     E    74_A     E    74_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     R    75_A     R    75_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     Y    76_A     Y    76_A     23   24   28     18   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     L    77_A     L    77_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     R    78_A     R    78_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     D    79_A     D    79_A     23   24   28     12   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     Q    80_A     Q    80_A     23   24   28     19   22   22   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_GDT     Q    81_A     Q    81_A     23   24   28      3    3   19   23   23   23   23   23   23   24   24   25   26   26   27   27   28   28   28   29 
LCS_AVERAGE  LCS_A:  33.19  (  29.14   31.55   38.89 )

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     19     22     22     23     23     23     23     23     23     24     24     25     26     26     27     27     28     28     28     29 
GDT PERCENT_AT  26.39  30.56  30.56  31.94  31.94  31.94  31.94  31.94  31.94  33.33  33.33  34.72  36.11  36.11  37.50  37.50  38.89  38.89  38.89  40.28
GDT RMS_LOCAL    0.31   0.37   0.37   0.58   0.58   0.58   0.58   0.58   0.58   1.49   1.49   2.78   3.06   3.06   3.57   3.57   4.27   4.71   4.27   5.74
GDT RMS_ALL_AT  31.81  31.79  31.79  31.81  31.81  31.81  31.81  31.81  31.81  31.87  31.87  30.77  30.92  30.92  30.45  30.45  30.00  28.77  30.00  28.19

# Checking swapping
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    33_A      Q    33_A    73.339     0    0.051   1.098    77.987    0.000    0.000
LGA    L    34_A      L    34_A    70.252     0    0.057   0.135    72.015    0.000    0.000
LGA    L    35_A      L    35_A    66.070     0    0.020   1.405    68.202    0.000    0.000
LGA    S    36_A      S    36_A    63.909     0    0.027   0.057    67.125    0.000    0.000
LGA    G    37_A      G    37_A    62.078     0    0.046   0.046    63.442    0.000    0.000
LGA    I    38_A      I    38_A    58.559     0    0.037   0.669    63.308    0.000    0.000
LGA    V    39_A      V    39_A    54.585     0    0.031   1.281    57.457    0.000    0.000
LGA    Q    40_A      Q    40_A    53.310     0    0.034   1.262    55.336    0.000    0.000
LGA    Q    41_A      Q    41_A    51.061     0    0.047   1.403    55.476    0.000    0.000
LGA    Q    42_A      Q    42_A    46.797     0    0.072   0.990    50.446    0.000    0.000
LGA    N    43_A      N    43_A    43.836     0    0.045   1.389    45.477    0.000    0.000
LGA    N    44_A      N    44_A    42.888     0    0.026   0.861    47.598    0.000    0.000
LGA    L    45_A      L    45_A    40.158     0    0.044   1.382    43.657    0.000    0.000
LGA    L    46_A      L    46_A    35.741     0    0.030   0.809    37.819    0.000    0.000
LGA    R    47_A      R    47_A    33.964     0    0.074   1.355    43.939    0.000    0.000
LGA    A    48_A      A    48_A    32.799     0    0.023   0.029    34.898    0.000    0.000
LGA    I    49_A      I    49_A    30.275     0    0.065   0.148    35.309    0.000    0.000
LGA    E    50_A      E    50_A    25.877     0    0.033   1.287    27.773    0.000    0.000
LGA    A    51_A      A    51_A    24.715     0    0.024   0.027    26.326    0.000    0.000
LGA    Q    52_A      Q    52_A    24.335     0    0.007   0.952    30.266    0.000    0.000
LGA    Q    53_A      Q    53_A    21.545     0    0.047   1.506    22.887    0.000    0.000
LGA    H    54_A      H    54_A    17.373     0    0.371   1.294    20.194    0.000    0.000
LGA    L    55_A      L    55_A    11.332     0    0.258   1.351    13.789    0.357    0.179
LGA    L    56_A      L    56_A    12.777     0    0.285   1.294    18.374    0.000    0.000
LGA    Q    57_A      Q    57_A    11.257     0    0.618   1.620    15.752    2.500    1.111
LGA    L    58_A      L    58_A     7.285     0    0.593   0.596    13.149   17.619    9.167
LGA    T    59_A      T    59_A     0.378     0    0.656   0.572     4.408   89.286   74.830
LGA    V    60_A      V    60_A     0.390     0    0.026   0.136     0.989  100.000   95.918
LGA    W    61_A      W    61_A     0.648     0    0.014   1.370     6.534   92.857   65.170
LGA    G    62_A      G    62_A     0.608     0    0.032   0.032     0.608   90.476   90.476
LGA    I    63_A      I    63_A     0.255     0    0.028   0.647     1.963  100.000   95.417
LGA    K    64_A      K    64_A     0.409     0    0.065   1.356     5.928  100.000   79.577
LGA    Q    65_A      Q    65_A     0.238     0    0.031   1.131     4.045  100.000   78.042
LGA    L    66_A      L    66_A     0.222     0    0.040   1.425     4.311  100.000   80.536
LGA    Q    67_A      Q    67_A     0.252     0    0.018   0.906     4.471  100.000   81.640
LGA    A    68_A      A    68_A     0.173     0    0.030   0.027     0.266  100.000  100.000
LGA    R    69_A      R    69_A     0.220     0    0.023   1.076     4.293  100.000   77.576
LGA    I    70_A      I    70_A     0.465     0    0.050   1.390     3.964  100.000   82.917
LGA    L    71_A      L    71_A     0.411     0    0.000   0.894     3.461  100.000   88.036
LGA    A    72_A      A    72_A     0.335     0    0.043   0.049     0.467  100.000  100.000
LGA    V    73_A      V    73_A     0.394     0    0.000   1.022     2.177  100.000   89.932
LGA    E    74_A      E    74_A     0.259     0    0.027   0.681     2.856  100.000   86.243
LGA    R    75_A      R    75_A     0.329     0    0.048   1.136     6.091   95.238   64.805
LGA    Y    76_A      Y    76_A     0.797     0    0.013   0.391     1.203   90.476   87.460
LGA    L    77_A      L    77_A     0.551     0    0.030   1.437     3.397   95.238   81.429
LGA    R    78_A      R    78_A     0.125     0    0.039   1.051     6.380  100.000   63.723
LGA    D    79_A      D    79_A     0.567     0    0.033   0.211     1.224   95.238   91.726
LGA    Q    80_A      Q    80_A     0.162     0    0.049   0.700     2.398   95.238   82.063
LGA    Q    81_A      Q    81_A     2.036     0    0.375   1.441     4.035   62.024   68.148

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     404    404  100.00                72
SUMMARY(RMSD_GDC):    18.287         18.171                 18.900           30.924   26.613

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   72    4.0     23    0.58    32.986    32.485     3.363

LGA_LOCAL      RMSD:   0.584  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  31.809  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:  18.287  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.978530 * X  +   0.195398 * Y  +   0.065564 * Z  + -142.143555
  Y_new =   0.177824 * X  +  -0.961232 * Y  +   0.210739 * Z  +  60.045509
  Z_new =   0.104200 * X  +  -0.194555 * Y  +  -0.975341 * Z  + 182.692780 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.179764 -0.104389 -2.944703   [DEG:   10.2997   -5.9811 -168.7191 ]
ZXZ:  2.839972  2.919059  2.649888   [DEG:  162.7184  167.2497  151.8274 ]
 
# END of job
