
#######################################################
#                                                     #
#                        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   62 (  466),  selected   62 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   62 , 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:    62       2_A - 63_A        2.10     2.10
  LCS_AVERAGE:     98.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       3_A - 63_A        1.98     2.11
  LCS_AVERAGE:     96.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      13_A - 36_A        0.99     2.75
  LONGEST_CONTINUOUS_SEGMENT:    24      14_A - 37_A        0.97     2.69
  LCS_AVERAGE:     29.16

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   62
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     H     2_A     H     2_A      3   54   62      0    3    3    3    8   17   29   45   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I     3_A     I     3_A      3   61   62      3    3    8   10   19   24   38   47   53   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D     4_A     D     4_A     20   61   62      7   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C     5_A     C     5_A     21   61   62      7   15   30   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D     6_A     D     6_A     21   61   62      7   19   32   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K     7_A     K     7_A     21   61   62      7   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E     8_A     E     8_A     22   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C     9_A     C     9_A     22   61   62      7   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    10_A     N    10_A     22   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    11_A     R    11_A     22   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    12_A     R    12_A     22   61   62      5   20   35   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    13_A     C    13_A     24   61   62      6   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    14_A     S    14_A     24   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    15_A     K    15_A     24   61   62      4   14   21   41   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    16_A     A    16_A     24   61   62      5   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    17_A     S    17_A     24   61   62      5   18   34   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    18_A     A    18_A     24   61   62      4    4   36   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    19_A     H    19_A     24   61   62      4   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    20_A     D    20_A     24   61   62      6   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    21_A     R    21_A     24   61   62      6   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    22_A     C    22_A     24   61   62      6   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    23_A     L    23_A     24   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    24_A     K    24_A     24   61   62      5   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    25_A     Y    25_A     24   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    26_A     C    26_A     24   61   62      5   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    27_A     G    27_A     24   61   62      4   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    28_A     I    28_A     24   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    29_A     C    29_A     24   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    30_A     C    30_A     24   61   62      5   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    31_A     E    31_A     24   61   62      4   13   34   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    32_A     K    32_A     24   61   62      4   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    33_A     C    33_A     24   61   62      7   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    34_A     N    34_A     24   61   62      7   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    35_A     C    35_A     24   61   62      5   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    36_A     V    36_A     24   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    37_A     P    37_A     24   61   62      7   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    38_A     P    38_A     23   61   62      7   19   37   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    39_A     G    39_A     21   61   62      7   19   34   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    40_A     T    40_A     11   61   62      7   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    41_A     Y    41_A      8   61   62      3    4   10   31   42   53   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    42_A     G    42_A     13   61   62      4    4   30   41   53   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    43_A     N    43_A     13   61   62      7   19   34   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    44_A     E    44_A     13   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    45_A     D    45_A     13   61   62      7   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    46_A     S    46_A     13   61   62      4   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    47_A     C    47_A     13   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    48_A     P    48_A     13   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    49_A     C    49_A     13   61   62      4   20   33   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    50_A     Y    50_A     13   61   62      7   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    51_A     A    51_A     13   61   62      8   20   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    52_A     N    52_A     13   61   62      8   20   37   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    53_A     L    53_A     13   61   62      4   19   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    54_A     K    54_A     13   61   62      3   13   31   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    55_A     N    55_A     12   61   62      5   16   31   47   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    56_A     S    56_A     12   61   62      4    8   18   29   47   56   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    57_A     K    57_A     12   61   62      5   12   29   40   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    58_A     G    58_A     12   61   62      5   12   27   40   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    59_A     G    59_A     12   61   62      5   13   31   49   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    60_A     H    60_A     12   61   62      4   13   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    61_A     K    61_A     12   61   62      4   12   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    62_A     C    62_A     12   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    63_A     P    63_A     12   61   62      6   18   38   51   55   57   60   60   60   62   62   62   62   62   62   62   62   62   62   62 
LCS_AVERAGE  LCS_A:  74.74  (  29.16   96.65   98.41 )

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      8     20     38     51     55     57     60     60     60     62     62     62     62     62     62     62     62     62     62     62 
GDT PERCENT_AT  12.70  31.75  60.32  80.95  87.30  90.48  95.24  95.24  95.24  98.41  98.41  98.41  98.41  98.41  98.41  98.41  98.41  98.41  98.41  98.41
GDT RMS_LOCAL    0.29   0.71   1.17   1.37   1.55   1.64   1.80   1.80   1.80   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10
GDT RMS_ALL_AT   2.60   2.80   2.31   2.27   2.16   2.15   2.14   2.14   2.14   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10

# Checking swapping
#   possible swapping detected:  D    20_A      D    20_A
#   possible swapping detected:  E    31_A      E    31_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    H     2_A      H     2_A     6.535     0    0.090   1.046     8.605    9.881   23.714
LGA    I     3_A      I     3_A     6.814     0    0.593   1.576    12.966   23.810   12.321
LGA    D     4_A      D     4_A     1.410     0    0.555   0.747     4.658   69.286   58.214
LGA    C     5_A      C     5_A     2.174     0    0.120   0.237     2.588   68.810   67.540
LGA    D     6_A      D     6_A     1.810     0    0.021   0.686     3.638   77.143   70.298
LGA    K     7_A      K     7_A     0.994     0    0.076   0.535     2.793   88.214   80.899
LGA    E     8_A      E     8_A     1.258     0    0.023   0.381     1.527   81.429   82.487
LGA    C     9_A      C     9_A     1.477     0    0.053   0.076     1.629   81.429   78.571
LGA    N    10_A      N    10_A     0.854     0    0.111   0.655     2.267   88.214   83.869
LGA    R    11_A      R    11_A     1.458     0    0.063   1.107     7.708   77.143   45.325
LGA    R    12_A      R    12_A     1.684     0    0.030   1.547     6.236   72.857   63.420
LGA    C    13_A      C    13_A     1.224     0    0.169   0.222     3.096   83.690   76.270
LGA    S    14_A      S    14_A     0.794     0    0.083   0.649     2.738   79.643   79.286
LGA    K    15_A      K    15_A     2.844     0    0.056   1.010     4.337   57.262   54.286
LGA    A    16_A      A    16_A     1.724     0    0.062   0.080     1.954   72.857   74.571
LGA    S    17_A      S    17_A     2.409     0    0.043   0.488     4.628   62.857   56.667
LGA    A    18_A      A    18_A     2.297     0    0.098   0.100     2.453   64.762   64.762
LGA    H    19_A      H    19_A     1.960     0    0.164   0.899     3.583   66.905   62.952
LGA    D    20_A      D    20_A     1.749     0    0.166   0.423     2.358   72.857   71.845
LGA    R    21_A      R    21_A     1.907     0    0.090   1.173     4.406   75.000   61.991
LGA    C    22_A      C    22_A     1.270     0    0.110   0.154     1.611   79.286   81.508
LGA    L    23_A      L    23_A     0.923     0    0.084   0.162     1.778   88.214   83.750
LGA    K    24_A      K    24_A     2.100     0    0.075   0.528     5.968   68.810   52.857
LGA    Y    25_A      Y    25_A     2.169     0    0.015   0.595     2.692   64.762   63.492
LGA    C    26_A      C    26_A     1.789     0    0.072   0.189     1.974   72.857   74.286
LGA    G    27_A      G    27_A     1.792     0    0.172   0.172     2.639   68.929   68.929
LGA    I    28_A      I    28_A     1.675     0    0.081   0.690     4.389   72.857   65.357
LGA    C    29_A      C    29_A     1.690     0    0.061   0.685     1.813   75.000   75.714
LGA    C    30_A      C    30_A     1.560     0    0.035   0.042     2.026   77.143   74.365
LGA    E    31_A      E    31_A     1.578     0    0.025   0.525     3.982   77.143   64.762
LGA    K    32_A      K    32_A     1.375     0    0.050   0.468     2.516   81.429   76.825
LGA    C    33_A      C    33_A     0.928     0    0.597   0.515     3.584   72.024   71.111
LGA    N    34_A      N    34_A     1.234     0    0.245   0.320     4.018   86.071   68.452
LGA    C    35_A      C    35_A     1.370     0    0.094   0.876     1.776   81.429   78.571
LGA    V    36_A      V    36_A     0.498     0    0.334   1.304     2.625   90.595   82.109
LGA    P    37_A      P    37_A     0.986     0    0.071   0.112     1.432   85.952   85.306
LGA    P    38_A      P    38_A     1.881     0    0.069   0.163     2.278   72.857   70.544
LGA    G    39_A      G    39_A     1.789     0    0.136   0.136     2.149   70.833   70.833
LGA    T    40_A      T    40_A     1.383     0    0.169   0.249     3.352   71.429   67.619
LGA    Y    41_A      Y    41_A     3.472     0    0.686   1.211     8.642   63.333   28.690
LGA    G    42_A      G    42_A     3.267     0    0.023   0.023     3.349   51.786   51.786
LGA    N    43_A      N    43_A     1.694     0    0.267   0.323     2.296   70.833   75.060
LGA    E    44_A      E    44_A     0.835     0    0.144   0.203     1.116   90.476   88.466
LGA    D    45_A      D    45_A     1.282     0    0.161   0.709     3.316   79.286   71.310
LGA    S    46_A      S    46_A     1.444     0    0.067   0.235     1.786   81.429   78.571
LGA    C    47_A      C    47_A     0.410     0    0.040   0.413     2.589   95.238   88.095
LGA    P    48_A      P    48_A     0.697     0    0.054   0.368     1.446   88.333   89.252
LGA    C    49_A      C    49_A     1.756     0    0.031   0.195     2.981   72.976   68.968
LGA    Y    50_A      Y    50_A     1.110     0    0.080   0.299     2.862   83.690   75.952
LGA    A    51_A      A    51_A     1.167     0    0.118   0.125     1.744   79.286   81.524
LGA    N    52_A      N    52_A     1.446     0    0.088   0.390     2.787   81.429   75.179
LGA    L    53_A      L    53_A     1.043     0    0.102   0.965     3.274   81.429   77.560
LGA    K    54_A      K    54_A     1.207     0    0.077   1.264     5.326   83.690   70.106
LGA    N    55_A      N    55_A     1.998     0    0.021   0.343     2.827   67.143   65.952
LGA    S    56_A      S    56_A     4.014     0    0.086   0.662     6.463   40.476   35.079
LGA    K    57_A      K    57_A     3.122     0    0.151   0.539     5.332   50.000   45.979
LGA    G    58_A      G    58_A     2.758     0    0.095   0.095     2.783   59.048   59.048
LGA    G    59_A      G    59_A     1.664     0    0.015   0.015     1.999   79.405   79.405
LGA    H    60_A      H    60_A     1.108     0    0.148   0.954     5.871   85.952   59.714
LGA    K    61_A      K    61_A     1.591     0    0.081   0.762     2.153   72.976   78.730
LGA    C    62_A      C    62_A     2.317     0    0.116   0.154     2.546   62.857   63.492
LGA    P    63_A      P    63_A     2.116     0    0.275   0.422     2.636   62.857   65.986

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     466    466  100.00                63
SUMMARY(RMSD_GDC):     2.103          2.111                  2.792           71.676   66.978

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   63    4.0     60    1.80    76.587    86.923     3.156

LGA_LOCAL      RMSD:   1.801  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.140  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   2.103  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.970820 * X  +   0.116822 * Y  +  -0.209432 * Z  +  -1.257297
  Y_new =   0.150748 * X  +   0.976487 * Y  +  -0.154103 * Z  +  -2.405726
  Z_new =   0.186505 * X  +  -0.181177 * Y  +  -0.965604 * Z  +  -5.243410 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.987544 -0.187604 -2.956118   [DEG:  171.1736  -10.7489 -169.3731 ]
ZXZ: -0.936438  2.878551  2.341705   [DEG:  -53.6539  164.9289  134.1698 ]
 
# END of job
