
#######################################################
#                                                     #
#                        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   43 (  321),  selected   43 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   43 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

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     K     3_F     K     3_F     43   43   43      6   38   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I     4_F     I     4_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     5_F     K     5_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R     6_F     R     6_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F     7_F     F     7_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F     8_F     F     8_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A     9_F     A     9_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_F     K    10_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    11_F     D    11_F     43   43   43     28   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    12_F     M    12_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    13_F     R    13_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_F     A    14_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    15_F     A    15_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    16_F     L    16_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    17_F     A    17_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Q    18_F     Q    18_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    19_F     V    19_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    20_F     K    20_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    21_F     D    21_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    22_F     T    22_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    23_F     L    23_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    24_F     G    24_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    25_F     S    25_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    26_F     D    26_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    27_F     A    27_F     43   43   43      8   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    28_F     V    28_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    29_F     I    29_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    30_F     M    30_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    31_F     S    31_F     43   43   43      8   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    32_F     N    32_F     43   43   43      5   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    33_F     K    33_F     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     K    34_F     K    34_F     43   43   43      3    6   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    35_F     V    35_F     43   43   43      3    6   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    36_F     N    36_F     43   43   43      3   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_F     G    37_F     43   43   43      8   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    38_F     G    38_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    39_F     I    39_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    40_F     E    40_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    41_F     I    41_F     43   43   43     30   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    42_F     V    42_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    43_F     A    43_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    44_F     A    44_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    45_F     V    45_F     43   43   43     28   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  87.76  (  87.76   87.76   87.76 )

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     31     40     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  63.27  81.63  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76
GDT RMS_LOCAL    0.33   0.48   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57
GDT RMS_ALL_AT   0.59   0.58   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K     3_F      K     3_F     1.283     0    0.130   1.026     5.200   86.190   66.349
LGA    I     4_F      I     4_F     0.423     0    0.074   0.100     0.688   97.619   96.429
LGA    K     5_F      K     5_F     0.380     0    0.031   0.990     2.326  100.000   86.138
LGA    R     6_F      R     6_F     0.244     0    0.013   1.279     8.136  100.000   65.368
LGA    F     7_F      F     7_F     0.303     0    0.022   0.095     0.424  100.000  100.000
LGA    F     8_F      F     8_F     0.326     0    0.048   1.275     7.096  100.000   64.416
LGA    A     9_F      A     9_F     0.336     0    0.059   0.092     0.606   97.619   98.095
LGA    K    10_F      K    10_F     0.644     0    0.017   1.087     3.840   92.857   81.376
LGA    D    11_F      D    11_F     0.556     0    0.089   1.121     3.392   97.619   85.595
LGA    M    12_F      M    12_F     0.294     0    0.014   1.162     3.604  100.000   88.333
LGA    R    13_F      R    13_F     0.499     0    0.058   1.585     7.786  100.000   65.455
LGA    A    14_F      A    14_F     0.306     0    0.012   0.015     0.428  100.000  100.000
LGA    A    15_F      A    15_F     0.261     0    0.046   0.055     0.460  100.000  100.000
LGA    L    16_F      L    16_F     0.313     0    0.022   1.096     2.513  100.000   89.048
LGA    A    17_F      A    17_F     0.435     0    0.064   0.075     0.448  100.000  100.000
LGA    Q    18_F      Q    18_F     0.468     0    0.030   0.137     1.126  100.000   93.704
LGA    V    19_F      V    19_F     0.349     0    0.021   0.108     0.441  100.000  100.000
LGA    K    20_F      K    20_F     0.099     0    0.029   0.978     3.795  100.000   85.714
LGA    D    21_F      D    21_F     0.105     0    0.050   0.842     3.026  100.000   85.952
LGA    T    22_F      T    22_F     0.256     0    0.192   0.258     1.169   95.357   97.347
LGA    L    23_F      L    23_F     0.297     0    0.164   1.063     2.358   97.619   90.000
LGA    G    24_F      G    24_F     0.434     0    0.069   0.069     0.562   97.619   97.619
LGA    S    25_F      S    25_F     0.430     0    0.072   0.094     0.731  100.000   96.825
LGA    D    26_F      D    26_F     0.321     0    0.483   0.864     4.130   93.214   75.119
LGA    A    27_F      A    27_F     0.989     0    0.203   0.261     1.844   83.810   83.333
LGA    V    28_F      V    28_F     0.547     0    0.037   0.084     1.069   97.619   93.265
LGA    I    29_F      I    29_F     0.396     0    0.011   0.461     1.882  100.000   93.036
LGA    M    30_F      M    30_F     0.416     0    0.052   0.140     1.285   97.619   94.107
LGA    S    31_F      S    31_F     0.584     0    0.035   0.540     2.517   92.857   85.000
LGA    N    32_F      N    32_F     1.030     0    0.404   1.226     3.955   77.619   70.774
LGA    K    33_F      K    33_F     0.802     0    0.130   1.088     4.632   88.214   74.709
LGA    K    34_F      K    34_F     1.141     0    0.056   0.735     2.943   83.690   75.132
LGA    V    35_F      V    35_F     1.227     0    0.064   1.240     3.538   85.952   76.190
LGA    N    36_F      N    36_F     0.949     0    0.130   1.134     5.783   85.952   64.405
LGA    G    37_F      G    37_F     0.771     0    0.229   0.229     0.771   97.619   97.619
LGA    G    38_F      G    38_F     0.252     0    0.061   0.061     0.577   97.619   97.619
LGA    I    39_F      I    39_F     0.457     0    0.086   1.288     3.158   95.238   80.655
LGA    E    40_F      E    40_F     0.436     0    0.054   0.263     0.905   95.238   93.651
LGA    I    41_F      I    41_F     0.626     0    0.049   1.243     3.149   97.619   84.583
LGA    V    42_F      V    42_F     0.177     0    0.051   1.115     2.531  100.000   88.844
LGA    A    43_F      A    43_F     0.262     0    0.064   0.066     0.354  100.000  100.000
LGA    A    44_F      A    44_F     0.176     0    0.033   0.032     0.212  100.000  100.000
LGA    V    45_F      V    45_F     0.521     0    0.021   0.931     2.767   95.238   84.762

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     321    321  100.00                49
SUMMARY(RMSD_GDC):     0.572          0.628                  1.765           84.237   76.461

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   43   49    4.0     43    0.57    86.224    87.272     6.402

LGA_LOCAL      RMSD:   0.572  Number of atoms:   43  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.572  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   0.572  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.767397 * X  +   0.335492 * Y  +   0.546394 * Z  +  20.833546
  Y_new =  -0.164191 * X  +   0.926591 * Y  +  -0.338334 * Z  + -104.717545
  Z_new =  -0.619792 * X  +   0.169924 * Y  +   0.766148 * Z  + -31.463427 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.210780  0.668478  0.218256   [DEG:  -12.0768   38.3010   12.5052 ]
ZXZ:  1.016370  0.697970 -1.303209   [DEG:   58.2337   39.9907  -74.6684 ]
 
# END of job
