
#######################################################
#                                                     #
#                        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        2.13     2.13
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38      23_A - 60_A        1.94     2.42
  LCS_AVERAGE:     55.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34      26_A - 59_A        0.98     3.17
  LCS_AVERAGE:     45.58

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   25   60      9   15   26   40   46   52   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   25   60     10   21   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   25   60     10   21   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   25   60     10   20   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   25   60     10   22   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   25   60     10   20   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   25   60     10   21   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   25   60     10   22   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   25   60     10   17   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   25   60     10   21   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   25   60      5   17   26   42   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   25   60      4   11   19   26   45   50   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   25   60      4   13   21   40   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   25   60      4   20   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     20   25   60      3    4    9   32   45   51   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     18   25   60      4    6    7    9   35   48   52   56   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   38   60      4    6   28   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      5   38   60      4    6    7   10   13   20   30   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      5   38   60      4   11   31   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     34   38   60      4   21   30   36   43   50   54   56   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     34   38   60     12   26   32   40   48   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     34   38   60     14   26   32   41   48   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     34   38   60     14   26   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     34   38   60     14   26   33   42   48   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     34   38   60     14   26   32   41   48   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     34   38   60     14   26   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     34   38   60     18   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     34   38   60     16   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     34   38   60     16   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     34   38   60     19   27   33   42   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     34   38   60     19   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     34   38   60      7   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     34   38   60      7   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     34   38   60      4   27   33   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     34   38   60      4   27   31   43   49   53   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     32   38   60      0    3    3    3   43   51   54   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  66.99  (  45.58   55.39  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     19     27     33     43     49     53     56     57     59     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  31.67  45.00  55.00  71.67  81.67  88.33  93.33  95.00  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    0.31   0.51   0.94   1.22   1.42   1.61   1.80   1.86   2.05   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13
GDT RMS_ALL_AT   3.33   3.34   2.63   2.22   2.17   2.20   2.14   2.14   2.14   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13

# Checking swapping
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     3.034     0    0.118   1.117     4.071   54.167   58.631
LGA    D     2_A      D     2_A     1.693     0    0.046   1.050     4.600   79.405   67.024
LGA    K     3_A      K     3_A     0.874     0    0.037   1.175     7.180   88.214   60.688
LGA    A     4_A      A     4_A     1.844     0    0.035   0.045     2.592   79.286   74.857
LGA    A     5_A      A     5_A     1.698     0    0.055   0.054     2.125   77.143   74.667
LGA    C     6_A      C     6_A     1.346     0    0.042   0.107     2.752   83.690   77.460
LGA    A     7_A      A     7_A     0.882     0    0.033   0.044     1.197   90.476   88.667
LGA    D     8_A      D     8_A     0.976     0    0.078   0.239     2.567   88.214   78.571
LGA    G     9_A      G     9_A     1.652     0    0.036   0.036     1.652   77.143   77.143
LGA    I    10_A      I    10_A     1.588     0    0.030   1.065     2.688   79.286   72.083
LGA    A    11_A      A    11_A     1.022     0    0.033   0.037     1.362   85.952   85.048
LGA    A    12_A      A    12_A     0.991     0    0.040   0.044     1.561   90.476   86.952
LGA    V    13_A      V    13_A     1.466     0    0.041   1.009     2.388   81.429   74.286
LGA    K    14_A      K    14_A     1.592     0    0.052   1.269     5.885   77.143   62.540
LGA    A    15_A      A    15_A     1.325     0    0.074   0.074     1.661   81.548   79.810
LGA    R    16_A      R    16_A     0.695     0    0.029   1.955    10.650   90.476   49.784
LGA    V    17_A      V    17_A     2.386     0    0.072   1.204     5.822   63.333   58.027
LGA    E    18_A      E    18_A     3.853     0    0.086   0.287     7.549   45.238   29.365
LGA    K    19_A      K    19_A     2.573     0    0.156   0.794     5.831   62.976   47.249
LGA    L    20_A      L    20_A     0.936     0    0.179   0.876     5.640   67.381   53.571
LGA    A    21_A      A    21_A     3.725     0    0.022   0.027     5.327   61.667   54.571
LGA    P    22_A      P    22_A     5.030     0    0.694   0.802     9.162   41.190   26.190
LGA    E    23_A      E    23_A     2.108     0    0.102   1.399     5.668   52.262   42.910
LGA    A    24_A      A    24_A     5.654     0    0.230   0.234     7.349   26.429   23.143
LGA    V    25_A      V    25_A     2.097     0    0.606   0.626     5.232   69.286   57.619
LGA    P    26_A      P    26_A     4.443     0    0.200   0.370     7.234   48.690   35.170
LGA    Q    27_A      Q    27_A     3.831     0    0.277   0.596     4.690   42.024   53.175
LGA    K    28_A      K    28_A     3.363     0    0.086   0.810     5.285   48.333   43.016
LGA    L    29_A      L    29_A     2.281     0    0.049   1.185     3.576   62.857   64.405
LGA    K    30_A      K    30_A     2.726     0    0.042   0.625     5.174   57.143   45.608
LGA    R    31_A      R    31_A     2.920     0    0.014   1.354    10.721   60.952   32.771
LGA    A    32_A      A    32_A     1.856     0    0.047   0.049     2.254   75.119   74.667
LGA    L    33_A      L    33_A     1.063     0    0.038   0.951     3.200   81.429   73.333
LGA    K    34_A      K    34_A     1.755     0    0.031   0.915     5.204   77.143   59.577
LGA    I    35_A      I    35_A     1.257     0    0.041   1.287     3.790   85.952   75.774
LGA    A    36_A      A    36_A     0.365     0    0.040   0.048     0.761   97.619   98.095
LGA    E    37_A      E    37_A     0.814     0    0.049   0.743     4.977   88.214   69.735
LGA    R    38_A      R    38_A     0.527     0    0.029   0.661     4.281   95.238   68.398
LGA    E    39_A      E    39_A     0.458     0    0.042   1.202     4.266   95.238   81.852
LGA    Q    40_A      Q    40_A     0.983     0    0.041   0.241     1.768   85.952   81.587
LGA    G    41_A      G    41_A     1.376     0    0.107   0.107     1.985   77.143   77.143
LGA    E    42_A      E    42_A     1.475     0    0.189   0.986     2.618   83.690   76.878
LGA    G    43_A      G    43_A     1.691     0    0.072   0.072     1.834   72.857   72.857
LGA    E    44_A      E    44_A     1.604     0    0.133   0.539     3.715   75.000   69.630
LGA    F    45_A      F    45_A     2.093     0    0.041   1.462     9.090   66.786   37.706
LGA    D    46_A      D    46_A     2.459     0    0.097   0.839     3.067   68.810   64.940
LGA    E    47_A      E    47_A     1.537     0    0.058   1.002     4.161   79.405   69.259
LGA    C    48_A      C    48_A     0.759     0    0.045   0.851     3.310   88.214   80.714
LGA    L    49_A      L    49_A     1.013     0    0.035   1.458     5.259   85.952   67.262
LGA    E    50_A      E    50_A     0.930     0    0.027   0.639     5.065   90.476   66.667
LGA    A    51_A      A    51_A     0.443     0    0.043   0.052     0.582   97.619   98.095
LGA    L    52_A      L    52_A     0.223     0    0.050   1.430     3.869  100.000   81.071
LGA    D    53_A      D    53_A     0.151     0    0.034   0.455     1.073  100.000   95.298
LGA    D    54_A      D    54_A     0.806     0    0.045   1.065     5.050   90.595   73.036
LGA    A    55_A      A    55_A     1.129     0    0.031   0.052     1.616   81.548   81.524
LGA    K    56_A      K    56_A     1.404     0    0.046   0.388     2.503   79.286   74.021
LGA    R    57_A      R    57_A     1.133     0    0.086   1.248     5.690   79.286   68.225
LGA    A    58_A      A    58_A     1.533     0    0.143   0.142     2.152   72.976   72.952
LGA    L    59_A      L    59_A     2.064     0    0.565   1.493     5.411   66.786   58.155
LGA    P    60_A      P    60_A     3.883     0    0.126   0.148     8.230   43.452   29.320

# 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):     2.132          2.017                  3.148           74.927   65.546

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.86    77.917    76.515     2.902

LGA_LOCAL      RMSD:   1.864  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.141  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.132  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.453734 * X  +   0.291962 * Y  +  -0.841952 * Z  +  26.029507
  Y_new =   0.714398 * X  +  -0.683947 * Y  +   0.147824 * Z  +  -5.239536
  Z_new =  -0.532692 * X  +  -0.668562 * Y  +  -0.518907 * Z  +   3.580720 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.004948  0.561778 -2.230827   [DEG:   57.5793   32.1875 -127.8169 ]
ZXZ: -1.744598  2.116368 -2.468823   [DEG:  -99.9581  121.2589 -141.4531 ]
 
# END of job
