
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        0.50     0.50
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.50     0.50
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.50     0.50
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     61   61   61     43   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     61   61   61     49   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     61   61   61      5   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     61   61   61     44   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     61   61   61     21   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     61   61   61      6   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     61   61   61      9   56   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     61   61   61     42   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     61   61   61     50   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     61   61   61      3    3    3   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
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     50     59     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  81.97  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.40   0.42   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50
GDT RMS_ALL_AT   0.51   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     0.412     0    0.450   0.453     2.158   90.833   85.619
LGA    T    33_A      T    33_A     0.663     0    0.078   0.308     1.294   90.476   89.184
LGA    M    34_A      M    34_A     0.536     0    0.038   1.097     2.411   92.857   84.226
LGA    A    35_A      A    35_A     0.457     0    0.090   0.107     0.896   95.238   94.286
LGA    D    36_A      D    36_A     0.950     0    0.124   0.331     2.894   95.238   80.060
LGA    L    37_A      L    37_A     0.228     0    0.030   0.166     0.622  100.000   98.810
LGA    K    38_A      K    38_A     0.415     0    0.054   0.695     1.893   97.619   90.794
LGA    M    39_A      M    39_A     0.389     0    0.021   0.830     2.691  100.000   89.048
LGA    Q    40_A      Q    40_A     0.240     0    0.008   0.857     4.249  100.000   83.492
LGA    A    41_A      A    41_A     0.271     0    0.079   0.091     0.488  100.000  100.000
LGA    V    42_A      V    42_A     0.358     0    0.067   0.120     0.595   97.619   98.639
LGA    K    43_A      K    43_A     0.307     0    0.015   0.085     0.444  100.000  100.000
LGA    E    44_A      E    44_A     0.275     0    0.173   0.258     1.023   95.357   97.937
LGA    I    45_A      I    45_A     0.118     0    0.019   0.097     0.757  100.000   98.810
LGA    C    46_A      C    46_A     0.196     0    0.120   0.132     0.712   97.619   98.413
LGA    Y    47_A      Y    47_A     0.135     0    0.032   0.213     1.578  100.000   90.714
LGA    E    48_A      E    48_A     0.125     0    0.013   0.929     3.748  100.000   79.471
LGA    V    49_A      V    49_A     0.427     0    0.052   0.068     0.588  100.000   95.918
LGA    A    50_A      A    50_A     0.363     0    0.086   0.084     0.664   97.619   98.095
LGA    L    51_A      L    51_A     0.415     0    0.180   0.272     2.130   97.619   87.500
LGA    A    52_A      A    52_A     0.457     0    0.041   0.038     0.659   97.619   96.190
LGA    D    53_A      D    53_A     0.368     0    0.038   0.321     1.555   97.619   89.583
LGA    F    54_A      F    54_A     0.353     0    0.075   0.067     0.668   95.238   98.268
LGA    R    55_A      R    55_A     0.715     0    0.100   1.531    10.121   95.238   54.892
LGA    H    56_A      H    56_A     0.288     0    0.069   0.332     0.999   97.619   96.190
LGA    G    57_A      G    57_A     0.626     0    0.065   0.065     0.626   97.619   97.619
LGA    R    58_A      R    58_A     0.313     0    0.057   1.104     5.096   97.619   74.632
LGA    A    59_A      A    59_A     0.158     0    0.049   0.046     0.221  100.000  100.000
LGA    E    60_A      E    60_A     0.153     0    0.015   0.543     1.683  100.000   93.862
LGA    I    61_A      I    61_A     0.231     0    0.015   0.087     0.436  100.000  100.000
LGA    E    62_A      E    62_A     0.177     0    0.034   0.208     0.737  100.000   96.825
LGA    A    63_A      A    63_A     0.381     0    0.018   0.019     0.470  100.000  100.000
LGA    L    64_A      L    64_A     0.365     0    0.213   0.436     1.826   97.619   88.512
LGA    A    65_A      A    65_A     0.233     0    0.016   0.019     0.472  100.000  100.000
LGA    A    66_A      A    66_A     0.441     0    0.038   0.040     0.655   97.619   96.190
LGA    L    67_A      L    67_A     0.238     0    0.035   0.774     2.963  100.000   91.131
LGA    K    68_A      K    68_A     0.241     0    0.036   0.291     1.893  100.000   92.857
LGA    M    69_A      M    69_A     0.332     0    0.031   0.560     1.440  100.000   95.357
LGA    R    70_A      R    70_A     0.244     0    0.087   1.261     2.946   97.619   84.545
LGA    E    71_A      E    71_A     0.510     0    0.093   0.571     1.688   97.619   91.693
LGA    L    72_A      L    72_A     0.428     0    0.036   0.171     0.592  100.000   98.810
LGA    C    73_A      C    73_A     0.337     0    0.080   0.225     1.013  100.000   96.905
LGA    R    74_A      R    74_A     0.489     0    0.301   0.738     6.259   90.833   64.978
LGA    T    75_A      T    75_A     0.459     0    0.129   0.193     1.448  100.000   94.626
LGA    Y    76_A      Y    76_A     0.793     0    0.684   0.615     2.362   84.048   86.071
LGA    G    83_A      G    83_A     1.210     0    0.239   0.239     1.210   88.214   88.214
LGA    D    84_A      D    84_A     0.201     0    0.065   0.608     1.396   97.619   94.107
LGA    A    85_A      A    85_A     0.565     0    0.035   0.034     0.860   95.238   94.286
LGA    W    86_A      W    86_A     0.290     0    0.043   0.081     0.885   97.619   95.238
LGA    R    87_A      R    87_A     0.505     0    0.022   0.260     0.944   95.238   92.208
LGA    A    88_A      A    88_A     0.318     0    0.144   0.166     0.982   97.619   98.095
LGA    V    89_A      V    89_A     0.304     0    0.063   0.109     0.559   97.619   97.279
LGA    A    90_A      A    90_A     0.297     0    0.059   0.069     0.371  100.000  100.000
LGA    R    91_A      R    91_A     0.352     0    0.043   0.361     0.843  100.000   96.537
LGA    D    92_A      D    92_A     0.164     0    0.043   0.275     1.006  100.000   97.679
LGA    V    93_A      V    93_A     0.304     0    0.021   0.063     0.504  100.000   98.639
LGA    W    94_A      W    94_A     0.309     0    0.027   0.083     0.695  100.000   93.878
LGA    D    95_A      D    95_A     0.434     0    0.111   0.466     1.008   92.976   91.845
LGA    T    96_A      T    96_A     0.503     0    0.041   1.163     2.462   97.619   87.211
LGA    V    97_A      V    97_A     0.486     0    0.460   0.370     2.103   88.810   90.884
LGA    G    98_A      G    98_A     2.059     0    0.356   0.356     2.059   79.643   79.643

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     0.499          0.533                  1.259           97.053   92.074

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    0.50    99.180    99.619    10.176

LGA_LOCAL      RMSD:   0.499  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.499  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.499  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.505707 * X  +   0.639099 * Y  +  -0.579494 * Z  +   3.346347
  Y_new =   0.796206 * X  +   0.087144 * Y  +  -0.598717 * Z  +  25.669371
  Z_new =  -0.332140 * X  +  -0.764172 * Y  +  -0.552924 * Z  + -12.965378 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.136658  0.338572 -2.197160   [DEG:  122.4215   19.3987 -125.8880 ]
ZXZ: -0.769084  2.156665 -2.731584   [DEG:  -44.0653  123.5678 -156.5083 ]
 
# END of job
