
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     60   60   60     46   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     30   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     30   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     31   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     46   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     51   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     37   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     51     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  85.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36
GDT RMS_ALL_AT   0.37   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36

# Checking swapping
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.784     0    0.054   0.254     1.532   90.476   86.012
LGA    D     2_A      D     2_A     0.313     0    0.015   0.464     2.349   97.619   90.893
LGA    K     3_A      K     3_A     0.354     0    0.022   0.553     1.641  100.000   92.804
LGA    A     4_A      A     4_A     0.407     0    0.025   0.029     0.507  100.000   98.095
LGA    A     5_A      A     5_A     0.182     0    0.054   0.073     0.435  100.000  100.000
LGA    C     6_A      C     6_A     0.131     0    0.016   0.051     0.151  100.000  100.000
LGA    A     7_A      A     7_A     0.064     0    0.033   0.040     0.165  100.000  100.000
LGA    D     8_A      D     8_A     0.182     0    0.019   0.089     0.535  100.000   98.810
LGA    G     9_A      G     9_A     0.123     0    0.051   0.051     0.199  100.000  100.000
LGA    I    10_A      I    10_A     0.201     0    0.020   0.049     0.316  100.000  100.000
LGA    A    11_A      A    11_A     0.227     0    0.033   0.045     0.279  100.000  100.000
LGA    A    12_A      A    12_A     0.144     0    0.016   0.017     0.266  100.000  100.000
LGA    V    13_A      V    13_A     0.229     0    0.031   0.061     0.348  100.000  100.000
LGA    K    14_A      K    14_A     0.292     0    0.072   0.180     0.567   97.619   97.884
LGA    A    15_A      A    15_A     0.146     0    0.063   0.059     0.435  100.000  100.000
LGA    R    16_A      R    16_A     0.249     0    0.018   0.170     1.373  100.000   95.714
LGA    V    17_A      V    17_A     0.247     0    0.035   0.062     0.284  100.000  100.000
LGA    E    18_A      E    18_A     0.168     0    0.021   0.941     3.354  100.000   81.852
LGA    K    19_A      K    19_A     0.330     0    0.061   1.066     4.860   97.619   81.799
LGA    L    20_A      L    20_A     0.340     0    0.027   0.210     0.621  100.000   96.429
LGA    A    21_A      A    21_A     0.270     0    0.015   0.026     0.436  100.000  100.000
LGA    P    22_A      P    22_A     0.529     0    0.028   0.044     0.837   92.857   94.558
LGA    E    23_A      E    23_A     0.690     0    0.050   0.987     2.424   90.476   80.847
LGA    A    24_A      A    24_A     0.657     0    0.064   0.076     0.751   90.476   90.476
LGA    V    25_A      V    25_A     0.405     0    0.030   0.058     0.500  100.000   98.639
LGA    P    26_A      P    26_A     0.319     0    0.048   0.085     0.513  100.000   98.639
LGA    Q    27_A      Q    27_A     0.300     0    0.012   1.146     4.510  100.000   82.646
LGA    K    28_A      K    28_A     0.188     0    0.047   0.689     2.723  100.000   92.116
LGA    L    29_A      L    29_A     0.276     0    0.021   1.128     2.702  100.000   89.286
LGA    K    30_A      K    30_A     0.350     0    0.012   0.072     0.525  100.000   98.942
LGA    R    31_A      R    31_A     0.346     0    0.037   1.265     6.974  100.000   69.351
LGA    A    32_A      A    32_A     0.379     0    0.044   0.056     0.385  100.000  100.000
LGA    L    33_A      L    33_A     0.353     0    0.030   0.052     0.398  100.000  100.000
LGA    K    34_A      K    34_A     0.274     0    0.064   0.642     2.843  100.000   90.053
LGA    I    35_A      I    35_A     0.362     0    0.094   0.097     0.451  100.000  100.000
LGA    A    36_A      A    36_A     0.363     0    0.017   0.018     0.422  100.000  100.000
LGA    E    37_A      E    37_A     0.269     0    0.022   0.204     0.541  100.000   98.942
LGA    R    38_A      R    38_A     0.308     0    0.063   0.708     2.801  100.000   90.996
LGA    E    39_A      E    39_A     0.358     0    0.036   1.120     3.930  100.000   85.714
LGA    Q    40_A      Q    40_A     0.302     0    0.048   0.174     0.929  100.000   97.884
LGA    G    41_A      G    41_A     0.130     0    0.052   0.052     0.194  100.000  100.000
LGA    E    42_A      E    42_A     0.362     0    0.130   0.233     0.971  100.000   95.767
LGA    G    43_A      G    43_A     0.223     0    0.035   0.035     0.355  100.000  100.000
LGA    E    44_A      E    44_A     0.275     0    0.064   0.280     1.518  100.000   92.857
LGA    F    45_A      F    45_A     0.501     0    0.022   0.073     0.536   97.619   98.268
LGA    D    46_A      D    46_A     0.570     0    0.066   1.121     3.977   95.238   80.536
LGA    E    47_A      E    47_A     0.370     0    0.035   1.067     3.429  100.000   85.608
LGA    C    48_A      C    48_A     0.148     0    0.014   0.093     0.300  100.000  100.000
LGA    L    49_A      L    49_A     0.312     0    0.036   0.108     0.547  100.000   98.810
LGA    E    50_A      E    50_A     0.203     0    0.032   0.229     0.932  100.000   98.942
LGA    A    51_A      A    51_A     0.155     0    0.021   0.025     0.276  100.000  100.000
LGA    L    52_A      L    52_A     0.356     0    0.015   0.059     0.568  100.000   98.810
LGA    D    53_A      D    53_A     0.247     0    0.018   0.754     3.279  100.000   84.940
LGA    D    54_A      D    54_A     0.198     0    0.019   0.205     0.791  100.000   98.810
LGA    A    55_A      A    55_A     0.400     0    0.007   0.011     0.512   97.619   98.095
LGA    K    56_A      K    56_A     0.676     0    0.033   0.564     1.589   92.857   85.608
LGA    R    57_A      R    57_A     0.304     0    0.013   0.672     3.468  100.000   90.519
LGA    A    58_A      A    58_A     0.570     0    0.030   0.035     0.945   92.857   92.381
LGA    L    59_A      L    59_A     0.526     0    0.044   0.154     1.301   95.238   90.595
LGA    P    60_A      P    60_A     0.617     0    0.028   0.346     1.007   90.476   89.184

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.361          0.358                  1.031           98.651   94.318

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.36   100.000   100.000    13.023

LGA_LOCAL      RMSD:   0.361  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.361  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.361  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.019359 * X  +  -0.501168 * Y  +   0.865133 * Z  +  13.546338
  Y_new =  -0.656116 * X  +   0.659280 * Y  +   0.367236 * Z  +   6.174961
  Z_new =  -0.754412 * X  +  -0.560518 * Y  +  -0.341587 * Z  +   6.933198 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.600293  0.854758 -2.118108   [DEG:  -91.6900   48.9740 -121.3587 ]
ZXZ:  1.972231  1.919401 -2.209794   [DEG:  113.0005  109.9736 -126.6119 ]
 
# END of job
