
#######################################################
#                                                     #
#                        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        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     51   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     27   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     27   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     52   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     27   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     52   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     41   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     27   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     51   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     52     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  86.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37
GDT RMS_ALL_AT   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37

# 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
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.537     0    0.448   1.017     5.360   84.524   62.560
LGA    D     2_A      D     2_A     0.195     0    0.054   0.526     2.496  100.000   93.274
LGA    K     3_A      K     3_A     0.472     0    0.044   0.546     1.784  100.000   90.741
LGA    A     4_A      A     4_A     0.456     0    0.061   0.070     0.530   97.619   96.190
LGA    A     5_A      A     5_A     0.221     0    0.040   0.050     0.457  100.000  100.000
LGA    C     6_A      C     6_A     0.275     0    0.014   0.035     0.334  100.000  100.000
LGA    A     7_A      A     7_A     0.173     0    0.034   0.037     0.253  100.000  100.000
LGA    D     8_A      D     8_A     0.294     0    0.030   0.077     0.762  100.000   96.429
LGA    G     9_A      G     9_A     0.175     0    0.020   0.020     0.328  100.000  100.000
LGA    I    10_A      I    10_A     0.232     0    0.013   0.022     0.323  100.000  100.000
LGA    A    11_A      A    11_A     0.260     0    0.027   0.033     0.277  100.000  100.000
LGA    A    12_A      A    12_A     0.192     0    0.027   0.025     0.359  100.000  100.000
LGA    V    13_A      V    13_A     0.284     0    0.015   0.040     0.462  100.000  100.000
LGA    K    14_A      K    14_A     0.336     0    0.052   0.159     0.633  100.000   97.884
LGA    A    15_A      A    15_A     0.150     0    0.050   0.046     0.445  100.000  100.000
LGA    R    16_A      R    16_A     0.177     0    0.022   0.828     4.039  100.000   82.511
LGA    V    17_A      V    17_A     0.159     0    0.029   0.032     0.236  100.000  100.000
LGA    E    18_A      E    18_A     0.123     0    0.026   0.916     3.340  100.000   81.005
LGA    K    19_A      K    19_A     0.237     0    0.073   1.100     4.866   97.619   82.646
LGA    L    20_A      L    20_A     0.302     0    0.028   0.193     0.467  100.000  100.000
LGA    A    21_A      A    21_A     0.499     0    0.028   0.033     0.568   95.238   94.286
LGA    P    22_A      P    22_A     0.603     0    0.058   0.065     0.973   90.476   90.476
LGA    E    23_A      E    23_A     0.652     0    0.036   0.984     2.368   90.476   81.746
LGA    A    24_A      A    24_A     0.586     0    0.037   0.040     0.774   95.238   94.286
LGA    V    25_A      V    25_A     0.296     0    0.019   0.050     0.352  100.000  100.000
LGA    P    26_A      P    26_A     0.287     0    0.010   0.087     0.412  100.000  100.000
LGA    Q    27_A      Q    27_A     0.219     0    0.015   0.940     3.547  100.000   85.026
LGA    K    28_A      K    28_A     0.142     0    0.038   0.850     3.831  100.000   80.476
LGA    L    29_A      L    29_A     0.209     0    0.016   1.129     2.790   97.619   88.095
LGA    K    30_A      K    30_A     0.342     0    0.014   0.103     0.700  100.000   98.942
LGA    R    31_A      R    31_A     0.335     0    0.027   1.262     6.964  100.000   68.788
LGA    A    32_A      A    32_A     0.283     0    0.021   0.023     0.342  100.000  100.000
LGA    L    33_A      L    33_A     0.349     0    0.051   0.084     0.538  100.000   97.619
LGA    K    34_A      K    34_A     0.362     0    0.051   0.640     2.757  100.000   91.058
LGA    I    35_A      I    35_A     0.344     0    0.059   0.056     0.374  100.000  100.000
LGA    A    36_A      A    36_A     0.336     0    0.023   0.021     0.482  100.000  100.000
LGA    E    37_A      E    37_A     0.348     0    0.047   0.334     0.953  100.000   97.884
LGA    R    38_A      R    38_A     0.319     0    0.052   0.122     0.982   97.619   95.671
LGA    E    39_A      E    39_A     0.320     0    0.018   1.082     3.871  100.000   85.714
LGA    Q    40_A      Q    40_A     0.329     0    0.045   1.192     4.500   97.619   84.127
LGA    G    41_A      G    41_A     0.161     0    0.038   0.038     0.226  100.000  100.000
LGA    E    42_A      E    42_A     0.420     0    0.142   0.252     1.095   97.619   93.704
LGA    G    43_A      G    43_A     0.343     0    0.079   0.079     0.475  100.000  100.000
LGA    E    44_A      E    44_A     0.376     0    0.080   0.979     4.321  100.000   84.339
LGA    F    45_A      F    45_A     0.573     0    0.012   0.050     0.788   95.238   92.208
LGA    D    46_A      D    46_A     0.582     0    0.062   0.514     1.607   92.857   89.464
LGA    E    47_A      E    47_A     0.460     0    0.040   1.046     3.051   97.619   84.550
LGA    C    48_A      C    48_A     0.132     0    0.024   0.102     0.251  100.000  100.000
LGA    L    49_A      L    49_A     0.361     0    0.032   0.086     0.583  100.000   98.810
LGA    E    50_A      E    50_A     0.238     0    0.026   0.216     1.011  100.000   96.878
LGA    A    51_A      A    51_A     0.155     0    0.020   0.027     0.283  100.000  100.000
LGA    L    52_A      L    52_A     0.425     0    0.035   0.063     0.569  100.000   97.619
LGA    D    53_A      D    53_A     0.371     0    0.043   0.082     0.425  100.000  100.000
LGA    D    54_A      D    54_A     0.236     0    0.017   0.561     1.967  100.000   90.893
LGA    A    55_A      A    55_A     0.402     0    0.025   0.030     0.615   95.238   96.190
LGA    K    56_A      K    56_A     0.747     0    0.033   0.658     1.562   90.476   84.550
LGA    R    57_A      R    57_A     0.266     0    0.036   0.275     0.871  100.000   97.403
LGA    A    58_A      A    58_A     0.531     0    0.067   0.063     1.057   90.595   90.571
LGA    L    59_A      L    59_A     0.528     0    0.030   0.186     1.354   95.238   90.595
LGA    P    60_A      P    60_A     0.604     0    0.033   0.327     1.069   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):     0.369          0.415                  1.155           98.157   93.240

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.37   100.000   100.000    12.792

LGA_LOCAL      RMSD:   0.369  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.369  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.369  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.114929 * X  +   0.417718 * Y  +   0.901279 * Z  +  12.767608
  Y_new =  -0.992659 * X  +  -0.082694 * Y  +  -0.088255 * Z  +   4.711308
  Z_new =   0.037664 * X  +  -0.904806 * Y  +   0.424156 * Z  +  10.319685 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.686062 -0.037673 -1.132434   [DEG:  -96.6042   -2.1585  -64.8837 ]
ZXZ:  1.473186  1.132767  3.099990   [DEG:   84.4073   64.9028  177.6163 ]
 
# END of job
