
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , 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:    63       1_A - 63_A        1.93     1.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.93     1.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      14_A - 38_A        0.98     2.42
  LCS_AVERAGE:     30.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     1_A     A     1_A     10   63   63      3    5   19   27   51   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      3   12   20   49   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     21   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     22   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   63   63      7   16   35   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     22   63   63      7   13   35   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     22   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     22   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     22   63   63      7   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     22   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     22   63   63      4   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     22   63   63      4   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     23   63   63      4   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   63   63      3    5   23   48   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   63   63      4   18   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   63   63      6   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   63   63      5   20   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   63   63      4   14   39   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   63   63      5   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   63   63     10   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   63   63      4   24   42   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   13   32   44   53   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    6   13   23   36   49   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      4    5   15   23   36   49   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      5   18   41   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      6   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      6   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      5   17   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      5   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   19   41   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   63   63     10   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   63   63      9   20   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   63   63      7   19   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   63   63      7   18   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   63   63      4   13   35   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   63   63      5   16   29   51   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   63   63      5    8   18   28   50   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   63   63      5   13   28   42   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   63   63      5   13   22   42   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     12   63   63      5   13   35   51   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     12   63   63      5   14   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      5   18   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.80  (  30.41  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     10     24     44     52     58     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  69.84  82.54  92.06  95.24  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.74   1.09   1.24   1.52   1.65   1.65   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93
GDT RMS_ALL_AT   2.46   2.61   2.15   2.09   1.97   1.96   1.96   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.338     0    0.126   0.181     3.744   59.286   56.095
LGA    H     2_A      H     2_A     2.098     0    0.022   0.695     4.029   71.190   59.429
LGA    I     3_A      I     3_A     0.192     0    0.087   0.913     2.927   90.595   86.369
LGA    D     4_A      D     4_A     1.267     0    0.072   1.066     3.960   81.548   70.714
LGA    C     5_A      C     5_A     1.981     0    0.087   0.249     2.464   72.857   71.508
LGA    D     6_A      D     6_A     1.540     0    0.019   0.563     3.356   79.405   74.345
LGA    K     7_A      K     7_A     0.478     0    0.088   0.529     2.691   92.857   83.016
LGA    E     8_A      E     8_A     1.148     0    0.059   0.381     1.622   81.548   85.503
LGA    C     9_A      C     9_A     1.429     0    0.070   0.080     1.678   81.429   78.571
LGA    N    10_A      N    10_A     0.734     0    0.126   0.302     1.410   85.952   84.821
LGA    R    11_A      R    11_A     1.562     0    0.023   1.507     5.671   75.000   60.606
LGA    R    12_A      R    12_A     1.471     0    0.016   1.465     6.583   81.429   62.251
LGA    C    13_A      C    13_A     1.194     0    0.256   0.271     3.017   81.548   76.270
LGA    S    14_A      S    14_A     1.034     0    0.069   0.669     3.260   77.381   75.000
LGA    K    15_A      K    15_A     3.062     0    0.152   1.026     4.637   57.262   52.169
LGA    A    16_A      A    16_A     1.826     0    0.059   0.070     2.220   70.833   72.952
LGA    S    17_A      S    17_A     2.028     0    0.026   0.690     3.863   68.810   63.889
LGA    A    18_A      A    18_A     2.004     0    0.054   0.060     2.181   68.810   68.000
LGA    H    19_A      H    19_A     1.687     0    0.208   1.149     3.469   68.929   65.905
LGA    D    20_A      D    20_A     1.366     0    0.192   0.221     1.909   81.429   78.214
LGA    R    21_A      R    21_A     1.615     0    0.075   1.301     8.155   77.143   50.087
LGA    C    22_A      C    22_A     1.142     0    0.082   0.127     1.437   83.690   85.952
LGA    L    23_A      L    23_A     1.030     0    0.064   0.155     1.764   85.952   82.619
LGA    K    24_A      K    24_A     2.280     0    0.086   0.427     5.087   66.786   53.757
LGA    Y    25_A      Y    25_A     2.211     0    0.023   0.689     3.213   64.762   63.651
LGA    C    26_A      C    26_A     1.773     0    0.101   0.202     2.030   70.833   72.937
LGA    G    27_A      G    27_A     1.886     0    0.175   0.175     2.832   66.905   66.905
LGA    I    28_A      I    28_A     1.892     0    0.108   0.729     4.772   72.857   64.643
LGA    C    29_A      C    29_A     1.720     0    0.051   0.685     1.742   75.000   75.714
LGA    C    30_A      C    30_A     1.517     0    0.051   0.078     2.050   77.143   74.365
LGA    E    31_A      E    31_A     1.430     0    0.034   0.418     3.599   81.429   69.101
LGA    K    32_A      K    32_A     1.015     0    0.061   1.071     6.409   88.214   64.709
LGA    C    33_A      C    33_A     0.825     0    0.599   0.519     3.575   74.286   72.619
LGA    N    34_A      N    34_A     1.039     0    0.230   0.402     3.358   88.333   72.917
LGA    C    35_A      C    35_A     1.025     0    0.023   0.384     1.699   85.952   81.587
LGA    V    36_A      V    36_A     0.677     0    0.147   0.172     1.621   90.476   85.374
LGA    P    37_A      P    37_A     0.397     0    0.070   0.317     0.700   95.238   95.918
LGA    P    38_A      P    38_A     1.456     0    0.046   0.102     1.722   79.286   78.980
LGA    G    39_A      G    39_A     2.154     0    0.157   0.157     2.855   62.976   62.976
LGA    T    40_A      T    40_A     4.574     0    0.551   0.486     5.769   34.762   31.973
LGA    Y    41_A      Y    41_A     4.701     0    0.154   1.026     6.634   32.857   26.786
LGA    G    42_A      G    42_A     4.434     0    0.592   0.592     5.553   31.786   31.786
LGA    N    43_A      N    43_A     1.242     0    0.285   0.347     1.986   77.143   80.417
LGA    E    44_A      E    44_A     0.509     0    0.136   0.629     3.394   95.238   76.190
LGA    D    45_A      D    45_A     1.022     0    0.093   1.060     5.771   83.690   64.762
LGA    S    46_A      S    46_A     1.336     0    0.148   0.163     1.752   79.286   80.000
LGA    C    47_A      C    47_A     0.750     0    0.085   0.341     1.607   92.857   87.619
LGA    P    48_A      P    48_A     0.488     0    0.065   0.325     1.366   92.976   93.265
LGA    C    49_A      C    49_A     1.787     0    0.043   0.227     3.108   72.976   67.778
LGA    Y    50_A      Y    50_A     0.927     0    0.125   0.349     2.332   90.476   83.889
LGA    A    51_A      A    51_A     1.010     0    0.136   0.139     1.522   81.548   83.333
LGA    N    52_A      N    52_A     1.197     0    0.092   0.172     2.421   85.952   78.393
LGA    L    53_A      L    53_A     1.134     0    0.091   0.658     2.251   79.286   79.405
LGA    K    54_A      K    54_A     1.444     0    0.103   1.275     5.100   81.429   68.254
LGA    N    55_A      N    55_A     1.973     0    0.052   0.091     2.874   67.143   70.060
LGA    S    56_A      S    56_A     4.078     0    0.156   0.676     6.650   37.619   32.540
LGA    K    57_A      K    57_A     3.060     0    0.176   0.546     5.271   50.000   46.720
LGA    G    58_A      G    58_A     2.856     0    0.147   0.147     2.856   57.143   57.143
LGA    G    59_A      G    59_A     1.712     0    0.026   0.026     2.010   75.119   75.119
LGA    H    60_A      H    60_A     1.586     0    0.180   1.001     5.813   75.000   55.095
LGA    K    61_A      K    61_A     1.366     0    0.038   0.746     1.837   77.143   82.646
LGA    C    62_A      C    62_A     1.888     0    0.033   0.073     2.272   75.000   71.587
LGA    P    63_A      P    63_A     1.642     0    0.330   0.481     2.167   70.833   71.701

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     1.926          1.949                  2.459           74.803   69.792

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.93    80.159    90.553     3.109

LGA_LOCAL      RMSD:   1.926  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.926  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.926  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.339267 * X  +   0.128083 * Y  +   0.931930 * Z  + -11.256179
  Y_new =   0.553130 * X  +   0.828487 * Y  +   0.087500 * Z  +  -0.108663
  Z_new =  -0.760884 * X  +   0.545164 * Y  +  -0.351925 * Z  + -12.694729 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.120980  0.864675  2.144029   [DEG:  121.5232   49.5422  122.8438 ]
ZXZ:  1.664413  1.930423 -0.949090   [DEG:   95.3639  110.6051  -54.3789 ]
 
# END of job
