
#######################################################
#                                                     #
#                        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   68 (  529),  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        0.88     0.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.88     0.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.88     0.88
  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     11   25   52   63   65   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     15   42   58   64   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     11   38   58   64   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     12   42   59   64   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     20   51   61   64   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     27   56   61   64   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     16   56   61   64   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     24   56   61   64   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     48   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     38   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     49   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     50   56   61   64   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     28   56   61   64   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     31   56   61   64   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     50   56   61   64   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     47   56   61   64   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     14   55   60   63   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      6   38   60   63   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   55   61   64   66   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     50     56     61     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  74.63  83.58  91.04  95.52  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    0.28   0.34   0.55   0.73   0.80   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88
GDT RMS_ALL_AT   1.00   1.03   0.92   0.89   0.89   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_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     3.066     0    0.028   0.058     3.236   55.476   54.841
LGA    P     3_A      P     3_A     2.162     0    0.019   0.024     2.872   66.905   63.810
LGA    E     4_A      E     4_A     2.139     0    0.028   0.983     3.695   68.810   62.487
LGA    E     5_A      E     5_A     1.883     0    0.053   1.032     7.395   77.381   53.228
LGA    Q     6_A      Q     6_A     1.397     0    0.022   0.652     2.326   83.810   79.735
LGA    K     7_A      K     7_A     0.741     0    0.030   0.635     2.382   92.857   83.862
LGA    Q     8_A      Q     8_A     0.945     0    0.010   1.494     5.926   92.857   68.201
LGA    M     9_A      M     9_A     0.753     0    0.026   0.680     1.291   90.476   87.083
LGA    L    10_A      L    10_A     0.428     0    0.036   0.078     1.051   97.619   94.107
LGA    G    11_A      G    11_A     0.609     0    0.076   0.076     0.609   97.619   97.619
LGA    E    12_A      E    12_A     0.375     0    0.030   0.808     3.112  100.000   87.354
LGA    A    13_A      A    13_A     0.220     0    0.037   0.041     0.457  100.000  100.000
LGA    I    14_A      I    14_A     0.160     0    0.022   0.062     0.237  100.000  100.000
LGA    Y    15_A      Y    15_A     0.179     0    0.031   0.190     0.835  100.000   96.825
LGA    P    16_A      P    16_A     0.126     0    0.045   0.040     0.204  100.000  100.000
LGA    K    17_A      K    17_A     0.178     0    0.052   0.723     2.989  100.000   90.265
LGA    V    18_A      V    18_A     0.195     0    0.035   0.055     0.269  100.000  100.000
LGA    A    19_A      A    19_A     0.279     0    0.045   0.046     0.332  100.000  100.000
LGA    A    20_A      A    20_A     0.374     0    0.027   0.036     0.565   97.619   98.095
LGA    S    21_A      S    21_A     0.267     0    0.063   0.076     0.738   97.619   96.825
LGA    Q    22_A      Q    22_A     0.231     0    0.084   0.187     0.712   97.619   95.767
LGA    P    23_A      P    23_A     0.513     0    0.021   0.040     0.619   95.238   94.558
LGA    E    24_A      E    24_A     0.330     0    0.092   0.615     2.194   92.976   89.841
LGA    L    25_A      L    25_A     0.294     0    0.030   0.044     0.539  100.000   98.810
LGA    A    26_A      A    26_A     0.383     0    0.038   0.046     0.512  100.000   98.095
LGA    G    27_A      G    27_A     0.500     0    0.038   0.038     0.500   97.619   97.619
LGA    K    28_A      K    28_A     0.300     0    0.009   1.194     6.071  100.000   74.603
LGA    L    29_A      L    29_A     0.180     0    0.018   0.133     0.880  100.000   97.619
LGA    T    30_A      T    30_A     0.359     0    0.030   0.067     0.590  100.000   98.639
LGA    G    31_A      G    31_A     0.422     0    0.058   0.058     0.422  100.000  100.000
LGA    M    32_A      M    32_A     0.152     0    0.011   0.133     0.568  100.000   98.810
LGA    I    33_A      I    33_A     0.302     0    0.051   0.077     0.515  100.000   98.810
LGA    L    34_A      L    34_A     0.196     0    0.034   0.076     0.477  100.000  100.000
LGA    E    35_A      E    35_A     0.601     0    0.120   1.060     4.725   90.595   68.995
LGA    L    36_A      L    36_A     0.597     0    0.012   0.075     0.647   90.476   91.667
LGA    P    37_A      P    37_A     0.801     0    0.048   0.315     1.696   90.476   87.959
LGA    V    38_A      V    38_A     0.872     0    0.024   0.056     0.988   90.476   90.476
LGA    T    39_A      T    39_A     0.818     0    0.015   0.048     0.861   90.476   90.476
LGA    E    40_A      E    40_A     0.540     0    0.030   0.832     3.834   92.857   81.005
LGA    L    41_A      L    41_A     0.636     0    0.018   0.089     0.709   90.476   91.667
LGA    L    42_A      L    42_A     0.765     0    0.035   0.054     1.210   90.476   87.083
LGA    H    43_A      H    43_A     0.522     0    0.034   1.108     2.667   90.476   85.667
LGA    L    44_A      L    44_A     0.623     0    0.018   0.130     0.756   90.476   92.857
LGA    L    45_A      L    45_A     0.995     0    0.072   1.373     3.070   88.214   78.810
LGA    E    46_A      E    46_A     0.962     0    0.028   0.813     3.207   90.476   73.862
LGA    E    47_A      E    47_A     0.776     0    0.041   1.077     3.985   90.476   75.873
LGA    S    48_A      S    48_A     0.451     0    0.025   0.630     2.480   97.619   92.540
LGA    E    49_A      E    49_A     0.548     0    0.075   0.270     1.375   95.238   89.577
LGA    A    50_A      A    50_A     0.387     0    0.017   0.018     0.500  100.000  100.000
LGA    L    51_A      L    51_A     0.146     0    0.026   0.127     0.589  100.000   98.810
LGA    D    52_A      D    52_A     0.146     0    0.017   0.067     0.197  100.000  100.000
LGA    A    53_A      A    53_A     0.309     0    0.037   0.044     0.586  100.000   98.095
LGA    K    54_A      K    54_A     0.196     0    0.004   0.552     1.521  100.000   93.810
LGA    V    55_A      V    55_A     0.094     0    0.032   0.049     0.168  100.000  100.000
LGA    N    56_A      N    56_A     0.132     0    0.006   0.117     0.312  100.000  100.000
LGA    E    57_A      E    57_A     0.110     0    0.037   0.711     2.370  100.000   85.238
LGA    A    58_A      A    58_A     0.408     0    0.026   0.029     0.529   97.619   96.190
LGA    L    59_A      L    59_A     0.491     0    0.007   0.335     1.062   95.238   92.917
LGA    E    60_A      E    60_A     0.535     0    0.047   0.263     1.881   90.476   86.614
LGA    V    61_A      V    61_A     0.635     0    0.010   0.052     0.924   92.857   91.837
LGA    L    62_A      L    62_A     1.153     0    0.019   1.398     3.566   83.690   76.726
LGA    K    63_A      K    63_A     1.227     0    0.015   0.515     3.225   81.429   74.286
LGA    E    64_A      E    64_A     0.601     0    0.012   0.902     2.446   90.476   80.106
LGA    Y    65_A      Y    65_A     1.193     0    0.024   1.032     6.094   79.405   60.238
LGA    Q    66_A      Q    66_A     2.121     0    0.125   0.178     5.030   68.810   53.016
LGA    Q    67_A      Q    67_A     1.936     0    0.217   0.488     4.816   72.976   59.841
LGA    N    68_A      N    68_A     1.214     0    0.276   1.176     4.436   64.762   57.679

# 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):     0.884          0.903                  1.564           92.381   87.185

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.88    94.776    97.624     6.808

LGA_LOCAL      RMSD:   0.884  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.884  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.884  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.654281 * X  +  -0.682238 * Y  +   0.326293 * Z  +  -1.036646
  Y_new =  -0.151737 * X  +  -0.541116 * Y  +  -0.827145 * Z  + -11.659685
  Z_new =   0.740872 * X  +   0.491675 * Y  +  -0.457563 * Z  +  -1.338065 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.227886 -0.834368  2.320274   [DEG:  -13.0569  -47.8058  132.9419 ]
ZXZ:  0.375740  2.046049  0.984890   [DEG:   21.5283  117.2300   56.4300 ]
 
# END of job
