
#######################################################
#                                                     #
#                        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   45 (  338),  selected   45 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   45 , 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:    45       3_F - 47_F        0.66     0.66
  LCS_AVERAGE:     91.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       3_F - 47_F        0.66     0.66
  LCS_AVERAGE:     91.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       3_F - 47_F        0.66     0.66
  LCS_AVERAGE:     91.84

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     45   45   45      8   38   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     I     4_F     I     4_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     K     5_F     K     5_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     R     6_F     R     6_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     F     7_F     F     7_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     F     8_F     F     8_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A     9_F     A     9_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     K    10_F     K    10_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     D    11_F     D    11_F     45   45   45     31   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     M    12_F     M    12_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     R    13_F     R    13_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    14_F     A    14_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    15_F     A    15_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     L    16_F     L    16_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    17_F     A    17_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     Q    18_F     Q    18_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     V    19_F     V    19_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     K    20_F     K    20_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     D    21_F     D    21_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     T    22_F     T    22_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     L    23_F     L    23_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     G    24_F     G    24_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     S    25_F     S    25_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     D    26_F     D    26_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    27_F     A    27_F     45   45   45      8   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     V    28_F     V    28_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     I    29_F     I    29_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     M    30_F     M    30_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     S    31_F     S    31_F     45   45   45      8   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     N    32_F     N    32_F     45   45   45      4   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     K    33_F     K    33_F     45   45   45     15   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     K    34_F     K    34_F     45   45   45      4    5   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     V    35_F     V    35_F     45   45   45      4    5   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     N    36_F     N    36_F     45   45   45      4   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     G    37_F     G    37_F     45   45   45      3   38   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     G    38_F     G    38_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     I    39_F     I    39_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     E    40_F     E    40_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     I    41_F     I    41_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     V    42_F     V    42_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    43_F     A    43_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     A    44_F     A    44_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     V    45_F     V    45_F     45   45   45     32   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     L    46_F     L    46_F     45   45   45      4   40   44   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_GDT     E    47_F     E    47_F     45   45   45      0    6   24   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45 
LCS_AVERAGE  LCS_A:  91.84  (  91.84   91.84   91.84 )

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     32     40     44     45     45     45     45     45     45     45     45     45     45     45     45     45     45     45     45     45 
GDT PERCENT_AT  65.31  81.63  89.80  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84  91.84
GDT RMS_LOCAL    0.32   0.45   0.59   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66
GDT RMS_ALL_AT   0.68   0.67   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66

# 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     1.286     0    0.089   1.113     5.825   86.190   65.238
LGA    I     4_F      I     4_F     0.393     0    0.110   0.119     0.537   95.238   96.429
LGA    K     5_F      K     5_F     0.475     0    0.039   0.991     2.325   95.238   82.063
LGA    R     6_F      R     6_F     0.168     0    0.012   1.224     7.433  100.000   68.571
LGA    F     7_F      F     7_F     0.252     0    0.026   0.081     0.385  100.000  100.000
LGA    F     8_F      F     8_F     0.231     0    0.047   1.249     7.067  100.000   64.416
LGA    A     9_F      A     9_F     0.306     0    0.062   0.082     0.553   97.619   98.095
LGA    K    10_F      K    10_F     0.634     0    0.029   1.081     3.716   95.238   82.434
LGA    D    11_F      D    11_F     0.544     0    0.114   1.214     3.694   97.619   85.893
LGA    M    12_F      M    12_F     0.302     0    0.014   1.132     3.981  100.000   86.131
LGA    R    13_F      R    13_F     0.478     0    0.053   1.577     7.894  100.000   65.455
LGA    A    14_F      A    14_F     0.282     0    0.024   0.030     0.433  100.000  100.000
LGA    A    15_F      A    15_F     0.355     0    0.065   0.072     0.550  100.000   98.095
LGA    L    16_F      L    16_F     0.403     0    0.028   1.108     2.661  100.000   90.060
LGA    A    17_F      A    17_F     0.513     0    0.046   0.055     0.551   90.476   90.476
LGA    Q    18_F      Q    18_F     0.518     0    0.030   0.362     1.619   95.238   88.624
LGA    V    19_F      V    19_F     0.409     0    0.015   0.102     0.510  100.000   98.639
LGA    K    20_F      K    20_F     0.251     0    0.029   0.975     3.989  100.000   85.714
LGA    D    21_F      D    21_F     0.203     0    0.046   0.378     0.961  100.000   97.619
LGA    T    22_F      T    22_F     0.311     0    0.151   1.154     2.374   97.619   88.571
LGA    L    23_F      L    23_F     0.264     0    0.173   1.072     2.389   97.619   90.000
LGA    G    24_F      G    24_F     0.369     0    0.062   0.062     0.545   97.619   97.619
LGA    S    25_F      S    25_F     0.413     0    0.045   0.123     0.780  100.000   96.825
LGA    D    26_F      D    26_F     0.196     0    0.483   0.792     3.750   93.214   75.893
LGA    A    27_F      A    27_F     0.962     0    0.215   0.269     1.934   81.548   83.333
LGA    V    28_F      V    28_F     0.652     0    0.044   0.092     1.224   95.238   90.612
LGA    I    29_F      I    29_F     0.314     0    0.036   0.458     1.910  100.000   95.417
LGA    M    30_F      M    30_F     0.390     0    0.062   0.126     1.300  100.000   95.298
LGA    S    31_F      S    31_F     0.528     0    0.020   0.540     2.611   92.857   86.508
LGA    N    32_F      N    32_F     0.933     0    0.438   1.227     4.071   79.881   70.179
LGA    K    33_F      K    33_F     0.705     0    0.130   1.069     4.527   88.214   75.556
LGA    K    34_F      K    34_F     1.205     0    0.069   0.746     2.788   83.690   75.979
LGA    V    35_F      V    35_F     1.342     0    0.048   1.239     3.522   83.690   74.898
LGA    N    36_F      N    36_F     0.860     0    0.184   1.083     5.017   83.810   65.417
LGA    G    37_F      G    37_F     1.435     0    0.241   0.241     1.435   88.214   88.214
LGA    G    38_F      G    38_F     0.193     0    0.055   0.055     0.614   95.238   95.238
LGA    I    39_F      I    39_F     0.402     0    0.085   1.353     3.249   95.238   80.655
LGA    E    40_F      E    40_F     0.395     0    0.079   0.272     0.970   95.238   95.767
LGA    I    41_F      I    41_F     0.497     0    0.033   1.233     3.142  100.000   85.774
LGA    V    42_F      V    42_F     0.266     0    0.030   1.107     2.748  100.000   88.639
LGA    A    43_F      A    43_F     0.157     0    0.052   0.057     0.265  100.000  100.000
LGA    A    44_F      A    44_F     0.162     0    0.042   0.038     0.190  100.000  100.000
LGA    V    45_F      V    45_F     0.325     0    0.065   1.030     2.682  100.000   87.755
LGA    L    46_F      L    46_F     0.778     0    0.600   1.096     3.753   82.143   78.155
LGA    E    47_F      E    47_F     1.944     0    0.613   1.029     3.367   66.905   64.974

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     338    338  100.00                49
SUMMARY(RMSD_GDC):     0.658          0.736                  1.774           86.752   79.005

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45   49    4.0     45    0.66    89.286    90.879     5.937

LGA_LOCAL      RMSD:   0.658  Number of atoms:   45  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.658  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:   0.658  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.935229 * X  +  -0.137218 * Y  +   0.326371 * Z  +  53.826138
  Y_new =   0.289575 * X  +   0.233911 * Y  +   0.928134 * Z  + -120.130447
  Z_new =  -0.203698 * X  +   0.962526 * Y  +  -0.179025 * Z  + -32.264111 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.841325  0.205134  1.754690   [DEG:  162.7959   11.7533  100.5364 ]
ZXZ:  2.803456  1.750792 -0.208552   [DEG:  160.6262  100.3130  -11.9491 ]
 
# END of job
