
#######################################################
#                                                     #
#                        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        0.95     0.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.95     0.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.95     0.95
  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   19   48   58   62   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     11   38   56   65   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   31   52   60   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     11   38   56   65   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     15   52   63   65   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     12   56   63   65   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     15   55   63   65   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     19   56   63   65   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     29   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     38   58   63   65   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     36   58   63   65   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     39   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     35   58   63   65   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     19   58   63   65   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     41   58   63   65   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     41   58   63   65   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     27   58   63   65   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     41   58   63   65   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     41   58   63   65   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     40   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     41   58   63   65   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     39   58   63   65   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     31   58   63   65   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     17   58   63   65   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     17   58   63   65   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     17   58   63   65   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     17   58   63   65   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     17   58   63   65   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     17   58   63   65   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     15   58   63   65   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   46   63   65   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     41     58     63     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  61.19  86.57  94.03  97.01  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    0.35   0.56   0.68   0.80   0.86   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95
GDT RMS_ALL_AT   1.12   1.10   1.01   0.97   0.96   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95

# Checking swapping
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_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     3.321     0    0.039   0.565     4.021   55.476   51.508
LGA    P     3_A      P     3_A     2.291     0    0.037   0.305     2.720   64.881   63.741
LGA    E     4_A      E     4_A     2.461     0    0.052   0.231     2.718   64.881   63.968
LGA    E     5_A      E     5_A     1.963     0    0.048   1.154     4.762   75.119   62.540
LGA    Q     6_A      Q     6_A     1.187     0    0.020   0.734     2.007   85.952   79.683
LGA    K     7_A      K     7_A     0.831     0    0.022   0.835     2.499   92.857   84.815
LGA    Q     8_A      Q     8_A     0.864     0    0.024   0.871     3.407   90.476   85.026
LGA    M     9_A      M     9_A     0.689     0    0.058   0.815     1.463   95.238   89.464
LGA    L    10_A      L    10_A     0.347     0    0.069   0.308     0.711   97.619   96.429
LGA    G    11_A      G    11_A     0.505     0    0.025   0.025     0.743   92.857   92.857
LGA    E    12_A      E    12_A     0.675     0    0.039   0.193     0.954   90.476   90.476
LGA    A    13_A      A    13_A     0.787     0    0.036   0.041     0.852   90.476   90.476
LGA    I    14_A      I    14_A     0.620     0    0.029   1.165     2.974   90.476   79.881
LGA    Y    15_A      Y    15_A     0.686     0    0.034   0.117     1.123   90.476   88.968
LGA    P    16_A      P    16_A     0.751     0    0.027   0.176     1.375   90.476   87.891
LGA    K    17_A      K    17_A     0.664     0    0.033   0.334     1.465   92.857   90.529
LGA    V    18_A      V    18_A     0.531     0    0.018   1.061     2.357   90.476   84.490
LGA    A    19_A      A    19_A     0.602     0    0.059   0.054     0.656   90.476   90.476
LGA    A    20_A      A    20_A     0.610     0    0.049   0.073     0.769   90.476   90.476
LGA    S    21_A      S    21_A     0.441     0    0.100   0.120     1.303  100.000   93.810
LGA    Q    22_A      Q    22_A     0.450     0    0.041   0.187     0.763   95.238   96.825
LGA    P    23_A      P    23_A     0.874     0    0.039   0.101     1.356   85.952   90.612
LGA    E    24_A      E    24_A     1.030     0    0.053   1.362     4.045   83.690   66.296
LGA    L    25_A      L    25_A     0.882     0    0.041   0.078     1.581   90.476   86.012
LGA    A    26_A      A    26_A     0.810     0    0.030   0.059     0.842   90.476   90.476
LGA    G    27_A      G    27_A     1.013     0    0.060   0.060     1.028   85.952   85.952
LGA    K    28_A      K    28_A     0.931     0    0.035   0.550     2.307   90.476   84.603
LGA    L    29_A      L    29_A     0.557     0    0.028   0.087     0.852   92.857   91.667
LGA    T    30_A      T    30_A     0.479     0    0.038   0.048     0.599   95.238   93.197
LGA    G    31_A      G    31_A     0.584     0    0.039   0.039     0.584   95.238   95.238
LGA    M    32_A      M    32_A     0.467     0    0.054   0.203     0.686  100.000   97.619
LGA    I    33_A      I    33_A     0.306     0    0.037   0.264     0.935  100.000   98.810
LGA    L    34_A      L    34_A     0.207     0    0.022   0.137     0.499  100.000  100.000
LGA    E    35_A      E    35_A     0.346     0    0.095   1.035     3.368   97.619   78.042
LGA    L    36_A      L    36_A     0.416     0    0.062   1.044     2.840   95.238   87.857
LGA    P    37_A      P    37_A     0.780     0    0.033   0.369     1.386   92.857   90.544
LGA    V    38_A      V    38_A     0.912     0    0.042   0.966     3.333   90.476   80.884
LGA    T    39_A      T    39_A     0.578     0    0.024   1.201     2.830   95.238   85.034
LGA    E    40_A      E    40_A     0.330     0    0.024   0.844     2.454  100.000   87.989
LGA    L    41_A      L    41_A     0.495     0    0.032   1.013     2.664   97.619   87.857
LGA    L    42_A      L    42_A     0.529     0    0.056   1.224     3.171   95.238   85.595
LGA    H    43_A      H    43_A     0.440     0    0.040   0.207     1.201  100.000   92.476
LGA    L    44_A      L    44_A     0.479     0    0.029   0.138     0.730   95.238   94.048
LGA    L    45_A      L    45_A     0.945     0    0.056   0.116     1.526   85.952   82.619
LGA    E    46_A      E    46_A     1.037     0    0.046   0.737     3.381   85.952   70.265
LGA    E    47_A      E    47_A     0.784     0    0.052   0.898     3.805   90.476   79.524
LGA    S    48_A      S    48_A     0.122     0    0.027   0.032     0.526  100.000   98.413
LGA    E    49_A      E    49_A     0.722     0    0.102   0.692     3.675   97.619   82.540
LGA    A    50_A      A    50_A     0.427     0    0.021   0.020     0.533  100.000   98.095
LGA    L    51_A      L    51_A     0.145     0    0.028   0.212     0.541  100.000   98.810
LGA    D    52_A      D    52_A     0.500     0    0.024   0.902     3.676   92.857   76.548
LGA    A    53_A      A    53_A     0.622     0    0.017   0.019     0.765   92.857   92.381
LGA    K    54_A      K    54_A     0.496     0    0.023   0.634     2.109   95.238   85.873
LGA    V    55_A      V    55_A     0.411     0    0.008   0.066     0.564  100.000   97.279
LGA    N    56_A      N    56_A     0.365     0    0.060   0.113     0.589  100.000   98.810
LGA    E    57_A      E    57_A     0.378     0    0.060   0.375     3.127  100.000   80.847
LGA    A    58_A      A    58_A     0.380     0    0.029   0.026     0.407  100.000  100.000
LGA    L    59_A      L    59_A     0.318     0    0.030   0.453     1.335   95.238   91.786
LGA    E    60_A      E    60_A     0.791     0    0.028   1.226     5.504   88.214   69.630
LGA    V    61_A      V    61_A     0.929     0    0.014   0.062     1.192   85.952   86.599
LGA    L    62_A      L    62_A     0.997     0    0.024   0.519     2.271   85.952   83.869
LGA    K    63_A      K    63_A     1.157     0    0.060   1.018     3.066   81.429   76.085
LGA    E    64_A      E    64_A     1.365     0    0.032   0.876     5.884   81.429   58.889
LGA    Y    65_A      Y    65_A     1.390     0    0.038   1.198     7.998   79.286   53.016
LGA    Q    66_A      Q    66_A     1.324     0    0.153   0.488     4.062   83.690   70.159
LGA    Q    67_A      Q    67_A     1.188     0    0.156   1.188     4.559   79.286   67.196
LGA    N    68_A      N    68_A     1.221     0    0.144   1.232     4.544   63.333   63.333

# 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):     0.953          0.972                  1.619           90.476   84.593

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.95    95.896    98.187     6.360

LGA_LOCAL      RMSD:   0.953  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.953  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.953  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.615509 * X  +  -0.506077 * Y  +  -0.604181 * Z  +  10.890649
  Y_new =  -0.783728 * X  +  -0.312122 * Y  +  -0.536982 * Z  +  17.110136
  Z_new =   0.083176 * X  +   0.804031 * Y  +  -0.588741 * Z  +   7.284749 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.905046 -0.083272  2.202831   [DEG:  -51.8553   -4.7712  126.2129 ]
ZXZ: -0.844217  2.200296  0.103082   [DEG:  -48.3700  126.0677    5.9062 ]
 
# END of job
