
#######################################################
#                                                     #
#                        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        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       2_A - 35_A        1.00     2.73
  LCS_AVERAGE:     41.37

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     29   63   63      3   24   35   45   56   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     34   63   63      7   26   37   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     34   63   63      7   24   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     34   63   63      7   24   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     34   63   63      6   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     34   63   63      5   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     34   63   63      5   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     34   63   63      3   15   35   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     34   63   63      3   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     34   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     34   63   63      5   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     34   63   63      5   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     34   63   63      4   19   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     34   63   63      4   19   38   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     34   63   63      5   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     34   63   63      6   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     34   63   63      7   19   38   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     34   63   63      4   16   33   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     34   63   63      4   24   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     34   63   63      3   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     34   63   63      7   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     31   63   63     10   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     10   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63     10   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63     10   26   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     10   63   63      3    7   11   26   44   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     10   63   63      3    7   11   19   32   44   53   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     10   63   63      3    6   11   16   28   42   53   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      3    8   26   50   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     12   63   63      5   18   38   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   18   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     12   63   63      5   18   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     14   63   63      5   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      5   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      3   19   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      3   19   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     16   63   63      4   19   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     16   63   63     10   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63     10   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      7   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      5   18   37   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      4   13   22   43   55   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      5   18   33   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      5   19   34   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     16   63   63      7   19   38   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     16   63   63      5   25   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      4   24   39   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      4   26   38   56   57   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     16   63   63      3    8   10   20   29   54   59   61   61   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.46  (  41.37  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     26     39     56     57     59     60     61     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  41.27  61.90  88.89  90.48  93.65  95.24  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.70   1.03   1.36   1.41   1.50   1.58   1.66   1.82   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89
GDT RMS_ALL_AT   2.17   2.67   2.05   1.92   1.91   1.91   1.90   1.90   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89

# 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     3.001     0    0.063   0.082     4.003   46.905   52.095
LGA    H     2_A      H     2_A     1.863     0    0.060   0.728     6.123   77.381   55.714
LGA    I     3_A      I     3_A     1.278     0    0.123   1.539     3.891   79.286   68.452
LGA    D     4_A      D     4_A     1.637     0    0.035   1.259     4.602   75.000   66.726
LGA    C     5_A      C     5_A     1.816     0    0.046   0.161     2.140   72.857   71.508
LGA    D     6_A      D     6_A     1.582     0    0.011   0.648     3.451   77.143   72.202
LGA    K     7_A      K     7_A     0.507     0    0.058   1.261     4.897   95.238   79.365
LGA    E     8_A      E     8_A     0.740     0    0.052   0.676     3.533   90.476   76.296
LGA    C     9_A      C     9_A     1.089     0    0.031   0.064     1.454   83.690   82.937
LGA    N    10_A      N    10_A     0.854     0    0.071   0.607     2.519   90.476   82.917
LGA    R    11_A      R    11_A     1.405     0    0.032   1.211     9.121   81.429   46.147
LGA    R    12_A      R    12_A     1.233     0    0.024   0.888     2.853   81.429   71.732
LGA    C    13_A      C    13_A     0.993     0    0.201   0.238     3.117   90.595   80.873
LGA    S    14_A      S    14_A     0.404     0    0.067   0.656     2.254   88.571   86.508
LGA    K    15_A      K    15_A     1.985     0    0.141   1.015     4.267   75.000   66.402
LGA    A    16_A      A    16_A     0.745     0    0.032   0.035     1.289   85.952   86.857
LGA    S    17_A      S    17_A     1.138     0    0.144   0.657     2.902   81.548   77.460
LGA    A    18_A      A    18_A     1.247     0    0.022   0.024     1.565   81.548   79.810
LGA    H    19_A      H    19_A     1.217     0    0.134   0.313     2.285   77.262   75.571
LGA    D    20_A      D    20_A     0.960     0    0.191   0.192     1.198   88.214   84.821
LGA    R    21_A      R    21_A     1.003     0    0.070   0.899     3.580   85.952   75.801
LGA    C    22_A      C    22_A     0.806     0    0.110   0.178     1.096   88.214   88.968
LGA    L    23_A      L    23_A     0.716     0    0.082   1.449     4.003   92.857   74.643
LGA    K    24_A      K    24_A     1.701     0    0.060   0.471     4.803   75.000   60.265
LGA    Y    25_A      Y    25_A     1.769     0    0.020   0.682     2.437   72.857   70.159
LGA    C    26_A      C    26_A     1.678     0    0.081   0.183     2.035   70.833   71.587
LGA    G    27_A      G    27_A     1.865     0    0.164   0.164     2.744   66.905   66.905
LGA    I    28_A      I    28_A     1.444     0    0.051   0.688     3.780   81.429   73.452
LGA    C    29_A      C    29_A     1.542     0    0.044   0.658     1.627   75.000   77.222
LGA    C    30_A      C    30_A     1.704     0    0.027   0.064     2.231   72.857   71.508
LGA    E    31_A      E    31_A     2.036     0    0.007   0.643     3.608   68.810   60.847
LGA    K    32_A      K    32_A     1.686     0    0.021   1.222     7.080   72.857   54.339
LGA    C    33_A      C    33_A     1.142     0    0.601   0.528     3.720   69.762   68.175
LGA    N    34_A      N    34_A     1.281     0    0.165   0.313     3.475   83.690   70.595
LGA    C    35_A      C    35_A     1.282     0    0.051   0.546     1.915   81.429   80.000
LGA    V    36_A      V    36_A     0.633     0    0.146   0.181     1.292   90.476   89.184
LGA    P    37_A      P    37_A     0.736     0    0.063   0.262     1.018   92.857   90.544
LGA    P    38_A      P    38_A     1.044     0    0.032   0.280     1.950   88.214   84.082
LGA    G    39_A      G    39_A     1.204     0    0.160   0.160     2.548   71.190   71.190
LGA    T    40_A      T    40_A     4.282     0    0.595   0.532     6.197   35.714   34.830
LGA    Y    41_A      Y    41_A     5.436     0    0.177   1.091    10.407   30.119   13.690
LGA    G    42_A      G    42_A     5.622     0    0.497   0.497     5.883   23.929   23.929
LGA    N    43_A      N    43_A     2.982     0    0.287   1.115     4.231   48.690   53.929
LGA    E    44_A      E    44_A     1.329     0    0.048   0.665     2.785   79.286   73.122
LGA    D    45_A      D    45_A     1.078     0    0.096   0.690     4.096   81.429   69.821
LGA    S    46_A      S    46_A     1.546     0    0.155   0.704     2.717   77.143   73.095
LGA    C    47_A      C    47_A     0.544     0    0.072   0.504     2.207   92.857   87.778
LGA    P    48_A      P    48_A     0.876     0    0.061   0.338     1.546   83.810   85.374
LGA    C    49_A      C    49_A     1.618     0    0.019   0.212     2.926   72.976   70.317
LGA    Y    50_A      Y    50_A     1.853     0    0.058   1.026     4.841   72.857   66.508
LGA    A    51_A      A    51_A     1.780     0    0.130   0.144     2.246   70.833   71.238
LGA    N    52_A      N    52_A     0.929     0    0.173   0.384     1.464   88.214   84.821
LGA    L    53_A      L    53_A     0.905     0    0.029   1.106     2.909   88.214   81.845
LGA    K    54_A      K    54_A     0.862     0    0.080   1.216     4.785   90.476   75.503
LGA    N    55_A      N    55_A     1.419     0    0.041   0.133     2.125   75.357   76.250
LGA    S    56_A      S    56_A     3.136     0    0.175   0.666     5.715   48.571   43.175
LGA    K    57_A      K    57_A     2.202     0    0.135   0.552     4.667   64.762   59.471
LGA    G    58_A      G    58_A     1.961     0    0.081   0.081     1.961   72.857   72.857
LGA    G    59_A      G    59_A     1.125     0    0.095   0.095     1.438   85.952   85.952
LGA    H    60_A      H    60_A     0.974     0    0.193   1.290     7.153   88.214   55.857
LGA    K    61_A      K    61_A     1.531     0    0.050   0.797     2.233   75.000   77.725
LGA    C    62_A      C    62_A     1.971     0    0.445   0.528     3.206   65.119   66.349
LGA    P    63_A      P    63_A     4.068     0    0.526   0.489     6.579   48.571   36.599

# 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):     1.889          1.919                  2.627           75.907   69.903

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.66    81.746    90.212     3.473

LGA_LOCAL      RMSD:   1.657  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.905  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.889  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.196722 * X  +  -0.621536 * Y  +   0.758284 * Z  +   4.001063
  Y_new =  -0.893477 * X  +   0.204823 * Y  +   0.399682 * Z  +   5.355345
  Z_new =  -0.403731 * X  +  -0.756136 * Y  +  -0.515035 * Z  +  -1.478037 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.354078  0.415591 -2.168753   [DEG:  -77.5830   23.8116 -124.2604 ]
ZXZ:  2.055878  2.111845 -2.651164   [DEG:  117.7931  120.9998 -151.9005 ]
 
# END of job
