
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.64     0.64
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     22   53   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     24   56   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     24   58   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     24   59   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     30   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     47   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     46   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     46   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     44   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     44   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     56   61   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3   11   43   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
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     56     61     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  83.58  91.04  97.01 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.35   0.52   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64
GDT RMS_ALL_AT   0.75   0.72   0.65   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     1.761     0    0.016   0.065     1.806   72.857   72.857
LGA    P     3_A      P     3_A     1.460     0    0.017   0.035     1.715   79.286   76.531
LGA    E     4_A      E     4_A     1.293     0    0.017   0.646     3.804   81.429   65.238
LGA    E     5_A      E     5_A     1.140     0    0.056   0.533     3.510   85.952   72.857
LGA    Q     6_A      Q     6_A     1.055     0    0.020   0.283     1.516   85.952   82.487
LGA    K     7_A      K     7_A     0.467     0    0.024   0.638     1.893   97.619   87.778
LGA    Q     8_A      Q     8_A     0.483     0    0.049   0.791     3.903   97.619   82.910
LGA    M     9_A      M     9_A     0.518     0    0.031   0.816     1.788   97.619   89.583
LGA    L    10_A      L    10_A     0.436     0    0.031   0.095     0.505   97.619   97.619
LGA    G    11_A      G    11_A     0.405     0    0.048   0.048     0.614   95.238   95.238
LGA    E    12_A      E    12_A     0.654     0    0.012   0.769     2.629   90.476   83.757
LGA    A    13_A      A    13_A     0.442     0    0.022   0.038     0.557   97.619   96.190
LGA    I    14_A      I    14_A     0.311     0    0.011   0.044     0.363  100.000  100.000
LGA    Y    15_A      Y    15_A     0.348     0    0.009   0.240     0.712  100.000   95.238
LGA    P    16_A      P    16_A     0.289     0    0.013   0.308     1.332  100.000   97.347
LGA    K    17_A      K    17_A     0.311     0    0.017   0.682     2.502  100.000   90.265
LGA    V    18_A      V    18_A     0.368     0    0.008   0.088     0.444  100.000  100.000
LGA    A    19_A      A    19_A     0.362     0    0.020   0.021     0.520   97.619   98.095
LGA    A    20_A      A    20_A     0.345     0    0.061   0.081     0.535   97.619   98.095
LGA    S    21_A      S    21_A     0.024     0    0.086   0.101     0.503  100.000   98.413
LGA    Q    22_A      Q    22_A     0.214     0    0.037   0.322     0.917  100.000   95.767
LGA    P    23_A      P    23_A     0.433     0    0.060   0.060     0.845   95.238   95.918
LGA    E    24_A      E    24_A     0.554     0    0.063   0.723     2.034   90.595   87.725
LGA    L    25_A      L    25_A     0.472     0    0.035   0.065     0.668  100.000   96.429
LGA    A    26_A      A    26_A     0.323     0    0.018   0.024     0.546  100.000   98.095
LGA    G    27_A      G    27_A     0.515     0    0.015   0.015     0.515   92.857   92.857
LGA    K    28_A      K    28_A     0.531     0    0.030   1.134     5.493   95.238   73.862
LGA    L    29_A      L    29_A     0.200     0    0.031   0.094     0.709  100.000   98.810
LGA    T    30_A      T    30_A     0.269     0    0.014   0.074     0.454  100.000  100.000
LGA    G    31_A      G    31_A     0.505     0    0.035   0.035     0.505   97.619   97.619
LGA    M    32_A      M    32_A     0.280     0    0.032   0.090     0.502  100.000   98.810
LGA    I    33_A      I    33_A     0.237     0    0.033   0.077     0.324  100.000  100.000
LGA    L    34_A      L    34_A     0.300     0    0.040   0.136     0.588  100.000   97.619
LGA    E    35_A      E    35_A     0.443     0    0.014   0.737     3.195   97.619   75.661
LGA    L    36_A      L    36_A     0.391     0    0.035   0.077     0.454  100.000  100.000
LGA    P    37_A      P    37_A     0.445     0    0.071   0.319     1.303   97.619   94.626
LGA    V    38_A      V    38_A     0.668     0    0.022   0.037     0.894   90.476   90.476
LGA    T    39_A      T    39_A     0.688     0    0.029   0.990     2.979   90.476   80.952
LGA    E    40_A      E    40_A     0.438     0    0.056   0.824     3.650   97.619   83.968
LGA    L    41_A      L    41_A     0.404     0    0.026   0.067     0.511   97.619   98.810
LGA    L    42_A      L    42_A     0.513     0    0.046   0.055     0.811   95.238   92.857
LGA    H    43_A      H    43_A     0.426     0    0.015   1.151     2.536  100.000   85.714
LGA    L    44_A      L    44_A     0.322     0    0.031   0.063     0.425  100.000  100.000
LGA    L    45_A      L    45_A     0.430     0    0.030   0.050     0.504  100.000   98.810
LGA    E    46_A      E    46_A     0.476     0    0.068   0.838     3.017  100.000   79.947
LGA    E    47_A      E    47_A     0.568     0    0.062   0.706     3.389   92.857   80.476
LGA    S    48_A      S    48_A     0.530     0    0.014   0.636     2.921   95.238   88.095
LGA    E    49_A      E    49_A     0.419     0    0.084   0.824     2.810  100.000   82.434
LGA    A    50_A      A    50_A     0.245     0    0.006   0.016     0.273  100.000  100.000
LGA    L    51_A      L    51_A     0.152     0    0.019   0.082     0.473  100.000  100.000
LGA    D    52_A      D    52_A     0.122     0    0.009   0.154     0.521  100.000   97.619
LGA    A    53_A      A    53_A     0.323     0    0.055   0.072     0.533  100.000   98.095
LGA    K    54_A      K    54_A     0.088     0    0.023   0.574     1.705  100.000   93.810
LGA    V    55_A      V    55_A     0.084     0    0.017   0.042     0.214  100.000  100.000
LGA    N    56_A      N    56_A     0.186     0    0.041   0.084     0.236  100.000  100.000
LGA    E    57_A      E    57_A     0.270     0    0.018   0.290     0.931  100.000   97.884
LGA    A    58_A      A    58_A     0.199     0    0.022   0.022     0.278  100.000  100.000
LGA    L    59_A      L    59_A     0.185     0    0.016   1.264     2.610  100.000   87.917
LGA    E    60_A      E    60_A     0.439     0    0.097   1.227     5.033   97.619   77.143
LGA    V    61_A      V    61_A     0.380     0    0.023   0.060     0.587   97.619   98.639
LGA    L    62_A      L    62_A     0.550     0    0.036   0.081     0.835   92.857   91.667
LGA    K    63_A      K    63_A     0.749     0    0.014   0.225     1.271   90.476   87.460
LGA    E    64_A      E    64_A     0.448     0    0.056   0.161     0.884   92.857   92.593
LGA    Y    65_A      Y    65_A     0.737     0    0.067   1.112     5.979   88.214   65.397
LGA    Q    66_A      Q    66_A     1.292     0    0.012   0.346     3.508   83.690   70.847
LGA    Q    67_A      Q    67_A     0.774     0    0.339   0.677     3.318   90.595   77.460
LGA    N    68_A      N    68_A     2.277     0    0.075   0.871     5.875   49.762   47.440

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.637          0.749                  1.319           95.291   90.012

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.64    97.761    99.070     9.094

LGA_LOCAL      RMSD:   0.637  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.637  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.637  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.180299 * X  +  -0.016537 * Y  +   0.983473 * Z  +   7.393571
  Y_new =  -0.982527 * X  +  -0.043914 * Y  +  -0.180864 * Z  +   2.996028
  Z_new =   0.046179 * X  +  -0.998898 * Y  +  -0.008330 * Z  +   6.485416 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.752283 -0.046195 -1.579136   [DEG: -100.3984   -2.6468  -90.4778 ]
ZXZ:  1.388925  1.579127  3.095396   [DEG:   79.5795   90.4773  177.3531 ]
 
# END of job
