
#######################################################
#                                                     #
#                        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   67 (  519),  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        0.81     0.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.81     0.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.81     0.81
  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     14   43   60   66   66   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     30   50   65   66   66   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     30   50   65   66   66   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     30   62   65   66   66   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   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     35   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     30   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     41   62   65   66   66   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     36   62   65   66   66   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     28   62   65   66   66   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     28   62   65   66   66   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     10   62   65   66   66   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     10   56   65   66   66   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     20   62   65   66   66   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    4    7   10   64   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     41     62     65     66     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  61.19  92.54  97.01  98.51  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.57   0.64   0.70   0.70   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81
GDT RMS_ALL_AT   1.04   0.86   0.83   0.82   0.82   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  D    52_A      D    52_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.074     0    0.056   0.744     3.611   68.810   63.889
LGA    P     3_A      P     3_A     1.371     0    0.009   0.282     1.566   81.429   80.272
LGA    E     4_A      E     4_A     1.178     0    0.021   0.815     4.871   85.952   66.667
LGA    E     5_A      E     5_A     0.910     0    0.062   0.743     3.876   88.214   75.556
LGA    Q     6_A      Q     6_A     0.984     0    0.013   0.280     1.318   90.476   88.466
LGA    K     7_A      K     7_A     0.336     0    0.016   0.639     2.065   97.619   87.937
LGA    Q     8_A      Q     8_A     0.196     0    0.040   0.466     1.823  100.000   94.868
LGA    M     9_A      M     9_A     0.429     0    0.017   0.824     1.783  100.000   88.631
LGA    L    10_A      L    10_A     0.614     0    0.042   0.846     1.910   90.476   84.940
LGA    G    11_A      G    11_A     0.525     0    0.046   0.046     0.788   92.857   92.857
LGA    E    12_A      E    12_A     0.801     0    0.017   0.769     1.934   90.476   85.556
LGA    A    13_A      A    13_A     0.681     0    0.020   0.021     0.726   95.238   94.286
LGA    I    14_A      I    14_A     0.421     0    0.020   0.052     0.456  100.000  100.000
LGA    Y    15_A      Y    15_A     0.447     0    0.017   0.264     0.903  100.000   93.651
LGA    P    16_A      P    16_A     0.457     0    0.014   0.032     0.561   95.238   94.558
LGA    K    17_A      K    17_A     0.554     0    0.009   0.702     2.417   90.476   85.820
LGA    V    18_A      V    18_A     0.654     0    0.014   0.048     0.688   90.476   90.476
LGA    A    19_A      A    19_A     0.603     0    0.020   0.020     0.927   90.476   90.476
LGA    A    20_A      A    20_A     0.829     0    0.031   0.052     0.976   90.476   90.476
LGA    S    21_A      S    21_A     0.582     0    0.141   0.561     2.039   88.214   84.683
LGA    Q    22_A      Q    22_A     0.521     0    0.013   0.160     1.398   92.857   90.529
LGA    P    23_A      P    23_A     0.760     0    0.072   0.078     1.236   88.214   87.891
LGA    E    24_A      E    24_A     0.750     0    0.046   0.133     1.251   88.214   91.587
LGA    L    25_A      L    25_A     0.668     0    0.039   0.059     0.866   90.476   90.476
LGA    A    26_A      A    26_A     0.534     0    0.015   0.014     0.596   92.857   92.381
LGA    G    27_A      G    27_A     0.788     0    0.028   0.028     0.788   90.476   90.476
LGA    K    28_A      K    28_A     0.751     0    0.020   1.174     5.689   90.476   71.217
LGA    L    29_A      L    29_A     0.400     0    0.031   0.082     0.857   97.619   97.619
LGA    T    30_A      T    30_A     0.358     0    0.012   0.053     0.410  100.000  100.000
LGA    G    31_A      G    31_A     0.777     0    0.060   0.060     0.777   92.857   92.857
LGA    M    32_A      M    32_A     0.566     0    0.041   0.139     0.969   90.476   90.476
LGA    I    33_A      I    33_A     0.117     0    0.052   0.081     0.347  100.000  100.000
LGA    L    34_A      L    34_A     0.379     0    0.043   0.110     0.497  100.000  100.000
LGA    E    35_A      E    35_A     0.638     0    0.036   1.058     3.970   90.476   71.005
LGA    L    36_A      L    36_A     0.603     0    0.037   0.123     0.787   90.476   92.857
LGA    P    37_A      P    37_A     0.724     0    0.027   0.038     0.789   90.476   90.476
LGA    V    38_A      V    38_A     0.805     0    0.009   0.148     1.195   90.476   89.184
LGA    T    39_A      T    39_A     0.862     0    0.041   0.125     1.390   90.476   86.599
LGA    E    40_A      E    40_A     0.559     0    0.041   0.587     2.223   95.238   83.915
LGA    L    41_A      L    41_A     0.452     0    0.021   0.065     0.566   95.238   94.048
LGA    L    42_A      L    42_A     0.594     0    0.064   0.068     0.701   90.476   90.476
LGA    H    43_A      H    43_A     0.638     0    0.010   1.022     3.171   90.476   80.381
LGA    L    44_A      L    44_A     0.452     0    0.027   0.124     0.461  100.000  100.000
LGA    L    45_A      L    45_A     0.482     0    0.066   0.085     0.520   97.619   97.619
LGA    E    46_A      E    46_A     0.744     0    0.086   0.719     3.383   90.476   74.074
LGA    E    47_A      E    47_A     0.905     0    0.067   0.686     3.429   90.476   79.418
LGA    S    48_A      S    48_A     0.823     0    0.016   0.635     3.103   90.476   83.730
LGA    E    49_A      E    49_A     0.803     0    0.102   0.646     2.048   90.476   80.741
LGA    A    50_A      A    50_A     0.458     0    0.009   0.010     0.535   97.619   98.095
LGA    L    51_A      L    51_A     0.370     0    0.023   0.245     1.050  100.000   96.488
LGA    D    52_A      D    52_A     0.413     0    0.039   0.850     2.889  100.000   86.667
LGA    A    53_A      A    53_A     0.632     0    0.057   0.072     0.741   90.476   90.476
LGA    K    54_A      K    54_A     0.575     0    0.024   0.293     1.028   90.476   91.587
LGA    V    55_A      V    55_A     0.419     0    0.023   0.041     0.459  100.000  100.000
LGA    N    56_A      N    56_A     0.519     0    0.043   0.660     2.051   92.857   85.119
LGA    E    57_A      E    57_A     0.677     0    0.011   0.704     3.551   90.476   76.720
LGA    A    58_A      A    58_A     0.658     0    0.022   0.023     0.737   90.476   90.476
LGA    L    59_A      L    59_A     0.478     0    0.034   1.303     2.573   95.238   85.476
LGA    E    60_A      E    60_A     0.669     0    0.073   1.089     4.596   90.476   75.714
LGA    V    61_A      V    61_A     0.641     0    0.017   0.125     0.861   90.476   90.476
LGA    L    62_A      L    62_A     0.660     0    0.040   0.729     2.672   90.476   85.179
LGA    K    63_A      K    63_A     0.760     0    0.018   0.848     4.097   90.476   74.709
LGA    E    64_A      E    64_A     0.544     0    0.037   0.915     4.435   90.476   74.497
LGA    Y    65_A      Y    65_A     0.801     0    0.019   0.707     3.489   85.952   74.246
LGA    Q    66_A      Q    66_A     1.197     0    0.025   0.959     4.372   85.952   74.762
LGA    Q    67_A      Q    67_A     0.368     0    0.312   0.977     3.174   92.976   79.524
LGA    N    68_A      N    68_A     3.322     0    0.653   0.826     7.043   34.643   33.095

# 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):     0.812          0.922                  1.439           91.407   86.379

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   67    4.0     67    0.81    97.761    98.985     7.346

LGA_LOCAL      RMSD:   0.812  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.812  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.812  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.485274 * X  +   0.658417 * Y  +   0.575322 * Z  +   9.060719
  Y_new =  -0.460930 * X  +  -0.751775 * Y  +   0.471569 * Z  +   3.784405
  Z_new =   0.743002 * X  +  -0.036343 * Y  +   0.668302 * Z  +   4.694790 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.381917 -0.837545 -0.054327   [DEG: -136.4738  -47.9878   -3.1127 ]
ZXZ:  2.257412  0.838873  1.619671   [DEG:  129.3402   48.0639   92.8003 ]
 
# END of job
