
#######################################################
#                                                     #
#                        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        1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       1_A - 35_A        0.99     2.79
  LCS_AVERAGE:     42.23

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     35   63   63      3   25   37   52   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     35   63   63      7   25   38   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     35   63   63      3   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     35   63   63      4   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     35   63   63      7   25   39   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     35   63   63      7   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     35   63   63      7   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     35   63   63     10   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     35   63   63      7   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     35   63   63     10   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     35   63   63      4   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     35   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     35   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     35   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     35   63   63      3   19   37   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     35   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     35   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     35   63   63      3   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     35   63   63      7   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     35   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     35   63   63      9   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     35   63   63     10   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     35   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     35   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     35   63   63      6   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     35   63   63      4   19   38   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     35   63   63      4   19   37   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     35   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     35   63   63      6   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     35   63   63      5   19   39   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     35   63   63      5   16   31   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     35   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     35   63   63      7   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     35   63   63      3   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     35   63   63      4   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     34   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63     11   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     33   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     33   63   63     11   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      6   63   63      3    5    9   26   43   57   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      6   63   63      3    6   12   18   27   42   51   59   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      4   63   63      3    4    5   10   17   27   36   46   60   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      3    6   16   36   53   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     12   63   63      5   18   37   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   19   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     12   63   63      5   16   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     14   63   63     11   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     15   63   63      9   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     15   63   63      3   16   36   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     15   63   63      5   19   38   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     15   63   63      4   19   38   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     15   63   63     11   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     15   63   63     11   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     15   63   63      6   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     15   63   63      6   18   36   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     15   63   63      5   10   24   46   56   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     15   63   63      6   18   34   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     15   63   63      6   19   35   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     15   63   63      6   22   39   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     15   63   63      5   24   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     15   63   63      5   25   40   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     15   63   63      6   25   39   56   57   59   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     15   63   63      3    3    9   22   47   55   59   61   61   62   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.74  (  42.23  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     11     25     40     56     57     59     59     61     61     62     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  63.49  88.89  90.48  93.65  93.65  96.83  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.69   1.06   1.35   1.37   1.48   1.48   1.65   1.65   1.79   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94
GDT RMS_ALL_AT   2.26   2.57   2.04   1.98   1.98   1.96   1.96   1.96   1.96   1.95   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94

# Checking swapping
#   possible swapping detected:  D     4_A      D     4_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.273     0    0.147   0.204     2.614   64.881   66.476
LGA    H     2_A      H     2_A     1.839     0    0.006   0.672     3.282   77.143   66.048
LGA    I     3_A      I     3_A     1.277     0    0.125   1.555     3.825   81.429   69.524
LGA    D     4_A      D     4_A     1.537     0    0.031   1.276     4.558   75.000   66.726
LGA    C     5_A      C     5_A     1.727     0    0.032   0.154     2.084   72.857   71.508
LGA    D     6_A      D     6_A     1.468     0    0.014   0.653     3.283   81.548   75.417
LGA    K     7_A      K     7_A     0.501     0    0.058   1.262     4.852   95.238   80.212
LGA    E     8_A      E     8_A     0.692     0    0.053   0.675     3.425   90.476   78.624
LGA    C     9_A      C     9_A     0.982     0    0.033   0.057     1.337   90.476   87.460
LGA    N    10_A      N    10_A     0.725     0    0.076   0.618     2.519   90.476   84.048
LGA    R    11_A      R    11_A     1.305     0    0.030   1.209     9.026   81.429   46.537
LGA    R    12_A      R    12_A     1.126     0    0.028   1.012     4.444   81.429   69.481
LGA    C    13_A      C    13_A     0.954     0    0.201   0.231     3.043   92.857   82.381
LGA    S    14_A      S    14_A     0.391     0    0.067   0.656     2.374   88.571   86.508
LGA    K    15_A      K    15_A     1.941     0    0.136   1.016     3.860   77.143   68.836
LGA    A    16_A      A    16_A     0.796     0    0.029   0.033     1.329   85.952   86.857
LGA    S    17_A      S    17_A     1.200     0    0.144   0.657     2.979   81.548   76.032
LGA    A    18_A      A    18_A     1.243     0    0.020   0.023     1.559   81.548   79.810
LGA    H    19_A      H    19_A     1.218     0    0.132   0.312     2.359   77.262   75.571
LGA    D    20_A      D    20_A     0.929     0    0.190   0.191     1.178   88.214   85.952
LGA    R    21_A      R    21_A     1.033     0    0.063   0.905     3.606   85.952   75.801
LGA    C    22_A      C    22_A     0.868     0    0.101   0.156     1.160   88.214   88.968
LGA    L    23_A      L    23_A     0.723     0    0.083   1.452     3.888   92.857   75.417
LGA    K    24_A      K    24_A     1.691     0    0.051   0.470     4.700   75.000   61.058
LGA    Y    25_A      Y    25_A     1.752     0    0.014   0.665     2.601   72.857   69.524
LGA    C    26_A      C    26_A     1.685     0    0.082   0.186     2.100   70.833   71.587
LGA    G    27_A      G    27_A     1.994     0    0.127   0.127     2.740   66.905   66.905
LGA    I    28_A      I    28_A     1.515     0    0.043   0.683     3.794   79.286   72.381
LGA    C    29_A      C    29_A     1.603     0    0.042   0.654     1.691   75.000   77.222
LGA    C    30_A      C    30_A     1.742     0    0.030   0.066     2.190   72.857   71.508
LGA    E    31_A      E    31_A     2.100     0    0.007   0.602     3.215   68.810   62.381
LGA    K    32_A      K    32_A     1.713     0    0.023   1.238     7.270   72.857   53.862
LGA    C    33_A      C    33_A     1.204     0    0.597   0.526     3.754   69.762   68.175
LGA    N    34_A      N    34_A     1.332     0    0.201   0.288     3.930   83.690   68.036
LGA    C    35_A      C    35_A     1.607     0    0.091   0.897     2.027   79.286   75.794
LGA    V    36_A      V    36_A     0.706     0    0.155   0.194     1.385   88.214   87.891
LGA    P    37_A      P    37_A     0.792     0    0.022   0.267     1.102   90.476   87.891
LGA    P    38_A      P    38_A     0.756     0    0.075   0.105     0.959   90.476   90.476
LGA    G    39_A      G    39_A     0.684     0    0.196   0.196     2.531   77.738   77.738
LGA    T    40_A      T    40_A     4.542     0    0.474   0.449     6.283   32.976   31.633
LGA    Y    41_A      Y    41_A     5.819     0    0.181   1.316     6.242   25.119   27.381
LGA    G    42_A      G    42_A     6.439     0    0.576   0.576     8.040   13.095   13.095
LGA    N    43_A      N    43_A     3.407     0    0.134   0.333     4.730   45.476   58.512
LGA    E    44_A      E    44_A     1.437     0    0.071   0.655     3.266   77.262   68.836
LGA    D    45_A      D    45_A     1.287     0    0.115   0.689     4.504   81.429   65.417
LGA    S    46_A      S    46_A     1.447     0    0.152   0.237     1.896   81.429   78.571
LGA    C    47_A      C    47_A     0.432     0    0.037   0.501     2.421   95.238   89.365
LGA    P    48_A      P    48_A     0.816     0    0.057   0.338     1.514   86.190   89.388
LGA    C    49_A      C    49_A     1.741     0    0.030   0.234     3.134   71.071   66.508
LGA    Y    50_A      Y    50_A     1.669     0    0.063   1.008     4.808   75.000   67.143
LGA    A    51_A      A    51_A     1.618     0    0.132   0.146     2.184   70.833   71.238
LGA    N    52_A      N    52_A     1.031     0    0.171   0.384     1.728   85.952   81.548
LGA    L    53_A      L    53_A     0.986     0    0.037   1.097     3.111   88.214   80.952
LGA    K    54_A      K    54_A     0.903     0    0.080   1.228     4.808   90.476   75.503
LGA    N    55_A      N    55_A     1.483     0    0.039   0.153     2.195   75.357   75.179
LGA    S    56_A      S    56_A     3.274     0    0.177   0.665     5.997   48.571   43.175
LGA    K    57_A      K    57_A     2.167     0    0.139   0.555     4.613   64.762   59.471
LGA    G    58_A      G    58_A     1.915     0    0.086   0.086     1.915   72.857   72.857
LGA    G    59_A      G    59_A     0.979     0    0.121   0.121     1.321   88.214   88.214
LGA    H    60_A      H    60_A     0.970     0    0.194   1.299     7.030   88.214   55.857
LGA    K    61_A      K    61_A     1.542     0    0.046   0.797     2.259   75.000   76.772
LGA    C    62_A      C    62_A     1.854     0    0.432   0.513     3.066   65.119   69.127
LGA    P    63_A      P    63_A     3.855     0    0.254   0.397     6.539   57.738   41.837

# 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):     1.942          1.975                  2.476           76.383   70.702

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.65    81.349    89.968     3.486

LGA_LOCAL      RMSD:   1.650  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.957  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.942  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.068262 * X  +  -0.821255 * Y  +   0.566463 * Z  +   7.258692
  Y_new =   0.072106 * X  +   0.562241 * Y  +   0.823824 * Z  +   1.423184
  Z_new =  -0.995058 * X  +   0.097081 * Y  +   0.020838 * Z  +  -2.185232 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.328815  1.471340  1.359361   [DEG:  133.4312   84.3016   77.8856 ]
ZXZ:  2.539236  1.549957 -1.473541   [DEG:  145.4875   88.8060  -84.4277 ]
 
# END of job
