
#######################################################
#                                                     #
#                        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   44 (  372),  selected   43 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   43 , 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:    43       4_A - 46_A        0.69     0.69
  LCS_AVERAGE:     44.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       4_A - 46_A        0.69     0.69
  LCS_AVERAGE:     44.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       4_A - 46_A        0.69     0.69
  LCS_AVERAGE:     44.33

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     E     4_A     E     4_A     43   43   43      8   28   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I     5_A     I     5_A     43   43   43     15   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     6_A     K     6_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G     7_A     G     7_A     43   43   43     21   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y     8_A     Y     8_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     9_A     E     9_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    10_A     Y    10_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Q    11_A     Q    11_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    12_A     L    12_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    13_A     Y    13_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    14_A     V    14_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    15_A     Y    15_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    16_A     A    16_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    17_A     S    17_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    18_A     D    18_A     43   43   43     19   39   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    19_A     K    19_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    20_A     L    20_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    21_A     F    21_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    22_A     R    22_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_A     A    23_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    24_A     D    24_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    25_A     I    25_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    26_A     S    26_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    27_A     E    27_A     43   43   43     25   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    28_A     D    28_A     43   43   43     15   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    29_A     Y    29_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    30_A     K    30_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    31_A     T    31_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    32_A     R    32_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    33_A     G    33_A     43   43   43     14   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    34_A     R    34_A     43   43   43     16   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    35_A     K    35_A     43   43   43     26   39   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    36_A     L    36_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    37_A     L    37_A     43   43   43     10   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    38_A     R    38_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    39_A     F    39_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    40_A     N    40_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    41_A     G    41_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_A     P    42_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    43_A     V    43_A     43   43   43     23   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    44_A     P    44_A     43   43   43     23   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    45_A     P    45_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    46_A     P    46_A     43   43   43     26   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  44.33  (  44.33   44.33   44.33 )

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     26     40     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  26.80  41.24  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33  44.33
GDT RMS_LOCAL    0.30   0.62   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   1.15   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  E     9_A      E     9_A
#   possible swapping detected:  Y    10_A      Y    10_A
#   possible swapping detected:  Y    13_A      Y    13_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  F    21_A      F    21_A
#   possible swapping detected:  F    39_A      F    39_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     4_A      E     4_A     1.405     4    0.165   0.228     2.291   81.786   46.402
LGA    I     5_A      I     5_A     0.454     0    0.064   0.134     0.776   92.857   95.238
LGA    K     6_A      K     6_A     0.843     0    0.043   1.130     5.388   90.476   75.079
LGA    G     7_A      G     7_A     0.143     0    0.039   0.039     0.348  100.000  100.000
LGA    Y     8_A      Y     8_A     0.570     0    0.050   0.077     0.807   95.238   92.063
LGA    E     9_A      E     9_A     0.784     0    0.019   0.592     3.163   90.476   75.714
LGA    Y    10_A      Y    10_A     0.996     0    0.069   0.170     1.255   85.952   87.460
LGA    Q    11_A      Q    11_A     0.671     0    0.066   1.183     5.485   95.238   74.497
LGA    L    12_A      L    12_A     0.330     0    0.025   0.993     2.448  100.000   91.012
LGA    Y    13_A      Y    13_A     0.317     0    0.043   0.248     1.799   97.619   89.206
LGA    V    14_A      V    14_A     0.419     0    0.040   1.250     2.566   97.619   86.122
LGA    Y    15_A      Y    15_A     0.542     0    0.068   0.201     0.827   92.857   91.270
LGA    A    16_A      A    16_A     0.635     0    0.072   0.089     0.884   90.476   90.476
LGA    S    17_A      S    17_A     0.667     0    0.026   0.046     1.050   88.214   88.968
LGA    D    18_A      D    18_A     1.270     0    0.086   0.459     1.778   79.286   80.357
LGA    K    19_A      K    19_A     0.670     0    0.047   1.021     3.567   90.476   80.529
LGA    L    20_A      L    20_A     0.361     0    0.028   1.277     2.803   97.619   87.857
LGA    F    21_A      F    21_A     0.231     0    0.018   0.108     0.727  100.000   96.537
LGA    R    22_A      R    22_A     0.268     0    0.036   1.387     5.098  100.000   73.203
LGA    A    23_A      A    23_A     0.266     0    0.030   0.030     0.587   97.619   96.190
LGA    D    24_A      D    24_A     0.848     0    0.036   0.139     1.893   92.857   86.071
LGA    I    25_A      I    25_A     0.886     0    0.032   0.619     1.686   90.476   87.143
LGA    S    26_A      S    26_A     0.535     0    0.013   0.131     0.765   90.476   90.476
LGA    E    27_A      E    27_A     0.417     0    0.034   0.199     1.824   97.619   89.683
LGA    D    28_A      D    28_A     0.519     0    0.014   0.205     0.619   92.857   95.238
LGA    Y    29_A      Y    29_A     0.698     0    0.031   0.130     1.338   90.476   86.706
LGA    K    30_A      K    30_A     1.042     0    0.034   0.963     3.056   83.690   77.037
LGA    T    31_A      T    31_A     0.812     0    0.031   0.060     0.866   90.476   90.476
LGA    R    32_A      R    32_A     0.765     0    0.048   1.626     7.254   90.476   62.338
LGA    G    33_A      G    33_A     0.668     0    0.227   0.227     0.936   92.857   92.857
LGA    R    34_A      R    34_A     0.904     0    0.035   1.269     3.742   85.952   79.654
LGA    K    35_A      K    35_A     1.119     0    0.020   1.094     3.947   88.214   76.402
LGA    L    36_A      L    36_A     0.807     0    0.108   0.185     1.358   85.952   90.595
LGA    L    37_A      L    37_A     0.751     0    0.227   0.931     2.086   92.857   85.119
LGA    R    38_A      R    38_A     0.567     0    0.145   0.721     2.019   95.238   84.978
LGA    F    39_A      F    39_A     0.398     0    0.014   0.099     0.556   97.619   99.134
LGA    N    40_A      N    40_A     0.510     0    0.020   1.122     2.695   95.238   86.488
LGA    G    41_A      G    41_A     0.611     0    0.053   0.053     0.809   90.476   90.476
LGA    P    42_A      P    42_A     0.354     0    0.012   0.396     1.592   97.619   92.041
LGA    V    43_A      V    43_A     0.658     0    0.044   0.209     1.300   90.476   89.184
LGA    P    44_A      P    44_A     0.530     0    0.039   0.192     0.659   92.857   91.837
LGA    P    45_A      P    45_A     0.347     0    0.052   0.171     0.688  100.000   97.279
LGA    P    46_A      P    46_A     0.353     0    0.103   0.415     0.763  100.000   97.279

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     357    357  100.00                97
SUMMARY(RMSD_GDC):     0.685          0.705                  1.365           41.119   38.316

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   44   97    4.0     43    0.69    43.557    44.086     5.476

LGA_LOCAL      RMSD:   0.685  Number of atoms:   43  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.685  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   0.685  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.065751 * X  +  -0.945330 * Y  +   0.319418 * Z  +  53.566013
  Y_new =  -0.996630 * X  +   0.077949 * Y  +   0.025543 * Z  +  49.532932
  Z_new =  -0.049045 * X  +  -0.316663 * Y  +  -0.947269 * Z  +  78.934906 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.636674  0.049065 -2.818981   [DEG:  -93.7745    2.8112 -161.5157 ]
ZXZ:  1.650593  2.815401 -2.987933   [DEG:   94.5720  161.3106 -171.1960 ]
 
# END of job
