
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        1.79     1.79
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.79     1.79
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.65     2.44
  LCS_AVERAGE:     45.81

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     20   60   60      9   22   30   43   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   60   60     11   22   38   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   60   60     13   34   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   60   60     14   25   44   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   60   60     14   32   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   60   60     20   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   60   60     18   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   60   60     17   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   60   60     22   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   60   60     14   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   60   60     23   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   60   60     23   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   60   60     14   33   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   60   60     14   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   60   60     14   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   60   60     13   27   44   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   60   60     14   22   39   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   60   60      4   33   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   60   60      4    5   24   47   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A      4   60   60      3    4    4    4    9   20   38   54   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   60   60      3   11   15   22   30   42   52   55   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   60   60      5   32   44   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      5   60   60      3    4    6   15   23   50   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      5   60   60      3    4    6   37   50   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   60   60      3   18   39   46   50   54   56   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60      3   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     27   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     26   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     19   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     23   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60     18   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60     19   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     17   37   45   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   60   60      3   19   41   51   54   56   57   58   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  81.94  (  45.81  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     27     37     45     51     54     56     57     58     59     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  45.00  61.67  75.00  85.00  90.00  93.33  95.00  96.67  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.53   0.76   0.98   1.14   1.30   1.39   1.46   1.72   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79
GDT RMS_ALL_AT   2.52   2.27   2.06   1.90   1.84   1.81   1.81   1.82   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     3.108     0    0.029   0.213     3.254   55.476   55.476
LGA    D     2_A      D     2_A     2.016     0    0.027   0.139     3.590   73.095   62.560
LGA    K     3_A      K     3_A     0.862     0    0.021   0.577     4.080   88.214   71.481
LGA    A     4_A      A     4_A     1.496     0    0.015   0.017     1.955   83.690   81.524
LGA    A     5_A      A     5_A     1.083     0    0.062   0.069     1.427   85.952   85.048
LGA    C     6_A      C     6_A     0.238     0    0.017   0.024     0.497  100.000  100.000
LGA    A     7_A      A     7_A     0.386     0    0.012   0.019     0.547  100.000   98.095
LGA    D     8_A      D     8_A     0.404     0    0.027   0.067     1.138  100.000   94.107
LGA    G     9_A      G     9_A     0.272     0    0.078   0.078     0.365  100.000  100.000
LGA    I    10_A      I    10_A     0.439     0    0.013   0.044     0.671   97.619   97.619
LGA    A    11_A      A    11_A     0.559     0    0.011   0.015     0.638   95.238   94.286
LGA    A    12_A      A    12_A     0.121     0    0.013   0.017     0.257  100.000  100.000
LGA    V    13_A      V    13_A     0.534     0    0.045   0.052     0.855   92.857   91.837
LGA    K    14_A      K    14_A     0.977     0    0.024   0.646     1.448   88.214   86.455
LGA    A    15_A      A    15_A     0.885     0    0.026   0.036     1.104   88.214   88.667
LGA    R    16_A      R    16_A     0.702     0    0.044   1.360     4.203   85.952   76.797
LGA    V    17_A      V    17_A     1.418     0    0.048   0.106     1.886   77.143   77.755
LGA    E    18_A      E    18_A     1.922     0    0.061   1.046     7.251   70.833   48.466
LGA    K    19_A      K    19_A     0.875     0    0.102   1.009     3.367   83.690   78.042
LGA    L    20_A      L    20_A     3.176     0    0.658   0.536     5.903   43.333   37.560
LGA    A    21_A      A    21_A     5.957     0    0.037   0.035     7.232   35.357   30.286
LGA    P    22_A      P    22_A     6.298     0    0.614   0.643    10.592   30.357   17.959
LGA    E    23_A      E    23_A     1.398     0    0.114   1.178     3.461   73.690   69.947
LGA    A    24_A      A    24_A     3.810     0    0.686   0.636     6.007   53.810   46.476
LGA    V    25_A      V    25_A     3.566     0    0.658   0.696     7.550   54.524   39.660
LGA    P    26_A      P    26_A     3.548     0    0.652   0.633     5.961   56.190   46.054
LGA    Q    27_A      Q    27_A     2.231     0    0.049   1.357     7.775   62.857   42.751
LGA    K    28_A      K    28_A     2.196     0    0.053   0.735     3.707   66.786   62.434
LGA    L    29_A      L    29_A     1.385     0    0.023   0.945     3.248   79.286   75.357
LGA    K    30_A      K    30_A     1.869     0    0.033   0.592     5.715   72.857   58.677
LGA    R    31_A      R    31_A     1.607     0    0.022   0.915     3.745   77.143   66.234
LGA    A    32_A      A    32_A     1.015     0    0.018   0.024     1.234   85.952   85.048
LGA    L    33_A      L    33_A     0.917     0    0.019   1.371     2.690   90.476   79.881
LGA    K    34_A      K    34_A     0.981     0    0.019   1.051     3.493   90.476   74.815
LGA    I    35_A      I    35_A     0.492     0    0.039   0.051     0.689   97.619   95.238
LGA    A    36_A      A    36_A     0.232     0    0.007   0.016     0.383  100.000  100.000
LGA    E    37_A      E    37_A     0.613     0    0.030   0.182     1.914   92.857   87.566
LGA    R    38_A      R    38_A     0.482     0    0.010   1.419     7.374   95.238   66.623
LGA    E    39_A      E    39_A     0.352     0    0.029   0.951     3.754   95.238   82.910
LGA    Q    40_A      Q    40_A     0.724     0    0.012   1.060     2.995   88.214   82.804
LGA    G    41_A      G    41_A     1.124     0    0.019   0.019     1.389   83.690   83.690
LGA    E    42_A      E    42_A     1.248     0    0.027   0.763     3.015   81.429   73.386
LGA    G    43_A      G    43_A     1.349     0    0.051   0.051     1.510   79.286   79.286
LGA    E    44_A      E    44_A     1.042     0    0.025   0.894     4.516   81.429   69.894
LGA    F    45_A      F    45_A     1.571     0    0.056   1.237     8.803   75.000   42.554
LGA    D    46_A      D    46_A     1.791     0    0.014   1.082     4.195   72.857   64.405
LGA    E    47_A      E    47_A     1.150     0    0.022   0.818     4.318   85.952   73.122
LGA    C    48_A      C    48_A     0.429     0    0.061   0.082     0.679   95.238   93.651
LGA    L    49_A      L    49_A     0.755     0    0.017   0.073     1.604   90.476   84.881
LGA    E    50_A      E    50_A     0.930     0    0.014   1.161     5.486   90.476   66.667
LGA    A    51_A      A    51_A     0.604     0    0.023   0.028     0.682   90.476   92.381
LGA    L    52_A      L    52_A     0.335     0    0.033   0.088     0.446  100.000  100.000
LGA    D    53_A      D    53_A     0.407     0    0.017   0.025     0.503  100.000   98.810
LGA    D    54_A      D    54_A     0.527     0    0.049   0.927     4.490   90.476   74.583
LGA    A    55_A      A    55_A     0.630     0    0.030   0.037     0.710   90.476   90.476
LGA    K    56_A      K    56_A     0.437     0    0.010   0.648     1.654   97.619   91.746
LGA    R    57_A      R    57_A     0.527     0    0.056   0.175     1.046   92.857   92.251
LGA    A    58_A      A    58_A     0.516     0    0.133   0.148     1.126   90.595   90.571
LGA    L    59_A      L    59_A     0.707     0    0.021   0.083     1.264   88.333   91.786
LGA    P    60_A      P    60_A     2.029     0    0.034   0.044     2.480   66.786   67.075

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     1.786          1.631                  2.469           82.532   75.962

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     58    1.46    85.833    92.449     3.729

LGA_LOCAL      RMSD:   1.456  Number of atoms:   58  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.817  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.786  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.419691 * X  +   0.817518 * Y  +   0.394364 * Z  +  -0.000741
  Y_new =  -0.231137 * X  +   0.516417 * Y  +  -0.824554 * Z  +  -4.911342
  Z_new =  -0.877744 * X  +   0.254906 * Y  +   0.405695 * Z  +   9.558726 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.503405  1.071133  0.560982   [DEG:  -28.8430   61.3714   32.1419 ]
ZXZ:  0.446118  1.153057 -1.288161   [DEG:   25.5607   66.0653  -73.8062 ]
 
# END of job
