
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.82     1.62
  LCS_AVERAGE:     88.92

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F     11   49   49      3    6   10   18   37   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      4   12   30   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      5   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     30   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49      6   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49     30   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49      4   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      7   24   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     21   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49      7   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49      8   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      4   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49      4   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      3   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     31   41   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      4   38   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      3   31   44   45   46   47   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F      5   49   49      3    4    5    7    8   24   46   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3   49   49      0    4    6    8   10   27   45   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  96.31  (  88.92  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     31     41     44     45     46     47     47     47     48     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  63.27  83.67  89.80  91.84  93.88  95.92  95.92  95.92  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.49   0.61   0.67   0.82   1.06   1.06   1.06   1.38   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56
GDT RMS_ALL_AT   1.67   1.69   1.65   1.63   1.62   1.63   1.63   1.63   1.58   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    21_F      D    21_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    40_F      E    40_F
#   possible swapping detected:  E    47_F      E    47_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F     4.468     0    0.159   1.149     6.010   40.238   37.202
LGA    G     2_F      G     2_F     2.671     0    0.109   0.109     3.422   57.262   57.262
LGA    K     3_F      K     3_F     0.804     0    0.165   1.066     5.979   85.952   66.984
LGA    I     4_F      I     4_F     0.532     0    0.068   0.139     1.163   90.595   88.274
LGA    K     5_F      K     5_F     0.436     0    0.031   1.008     2.832  100.000   83.333
LGA    R     6_F      R     6_F     0.681     0    0.021   0.981     6.359   90.476   66.580
LGA    F     7_F      F     7_F     0.611     0    0.021   0.096     0.922   90.476   91.342
LGA    F     8_F      F     8_F     0.544     0    0.000   1.309     6.985   92.857   61.602
LGA    A     9_F      A     9_F     0.338     0    0.041   0.056     0.466  100.000  100.000
LGA    K    10_F      K    10_F     0.421     0    0.027   1.046     4.902  100.000   80.265
LGA    D    11_F      D    11_F     1.103     0    0.081   0.944     3.028   90.595   79.940
LGA    M    12_F      M    12_F     0.563     0    0.007   1.096     4.038   95.238   82.976
LGA    R    13_F      R    13_F     0.329     0    0.070   1.572     7.839  100.000   65.455
LGA    A    14_F      A    14_F     0.331     0    0.028   0.030     0.431  100.000  100.000
LGA    A    15_F      A    15_F     0.331     0    0.063   0.072     0.410  100.000  100.000
LGA    L    16_F      L    16_F     0.194     0    0.021   1.091     2.320  100.000   90.000
LGA    A    17_F      A    17_F     0.610     0    0.055   0.062     0.755   92.857   92.381
LGA    Q    18_F      Q    18_F     0.676     0    0.031   0.512     2.031   90.476   87.619
LGA    V    19_F      V    19_F     0.447     0    0.037   0.105     0.473  100.000  100.000
LGA    K    20_F      K    20_F     0.198     0    0.019   0.909     3.784  100.000   85.714
LGA    D    21_F      D    21_F     0.494     0    0.025   0.505     1.632   97.619   91.845
LGA    T    22_F      T    22_F     0.642     0    0.155   1.130     2.608   90.476   83.197
LGA    L    23_F      L    23_F     0.606     0    0.143   1.079     2.820   95.238   86.488
LGA    G    24_F      G    24_F     0.579     0    0.078   0.078     0.843   95.238   95.238
LGA    S    25_F      S    25_F     0.456     0    0.070   0.615     3.029   97.619   88.492
LGA    D    26_F      D    26_F     0.969     0    0.522   1.241     5.538   88.214   69.286
LGA    A    27_F      A    27_F     1.681     0    0.202   0.269     2.268   70.833   71.238
LGA    V    28_F      V    28_F     1.089     0    0.046   0.093     1.447   85.952   84.014
LGA    I    29_F      I    29_F     0.709     0    0.018   0.616     2.891   90.476   86.310
LGA    M    30_F      M    30_F     0.892     0    0.039   0.630     1.919   88.214   86.012
LGA    S    31_F      S    31_F     0.855     0    0.052   0.752     3.661   88.214   79.603
LGA    N    32_F      N    32_F     1.232     0    0.470   0.463     2.923   77.619   79.583
LGA    K    33_F      K    33_F     0.539     0    0.060   0.887     3.191   90.476   77.460
LGA    K    34_F      K    34_F     0.969     0    0.064   0.752     3.071   88.214   77.302
LGA    V    35_F      V    35_F     0.887     0    0.050   1.220     3.139   90.476   81.020
LGA    N    36_F      N    36_F     0.767     0    0.074   1.186     5.515   92.857   70.119
LGA    G    37_F      G    37_F     0.341     0    0.212   0.212     0.779   97.619   97.619
LGA    G    38_F      G    38_F     0.500     0    0.082   0.082     0.587   95.238   95.238
LGA    I    39_F      I    39_F     0.437     0    0.087   1.299     3.092   95.238   80.655
LGA    E    40_F      E    40_F     0.496     0    0.074   0.345     0.994   95.238   93.651
LGA    I    41_F      I    41_F     0.775     0    0.058   1.250     3.181   90.476   79.881
LGA    V    42_F      V    42_F     0.317     0    0.049   1.042     2.509   95.238   86.122
LGA    A    43_F      A    43_F     0.666     0    0.079   0.090     0.786   92.857   92.381
LGA    A    44_F      A    44_F     0.609     0    0.043   0.049     0.673   90.476   90.476
LGA    V    45_F      V    45_F     0.870     0    0.036   1.265     3.247   92.857   82.381
LGA    L    46_F      L    46_F     1.494     0    0.619   1.022     4.697   64.762   59.524
LGA    E    47_F      E    47_F     1.554     0    0.305   0.777     5.197   62.619   53.915
LGA    H    48_F      H    48_F     5.667     0    0.263   1.201    13.673   25.833   10.810
LGA    H    49_F      H    49_F     6.729     0    0.240   1.249     9.427   10.238    9.095

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):     1.557          1.652                  2.631           86.805   78.692

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     47    1.06    92.857    96.178     4.045

LGA_LOCAL      RMSD:   1.062  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.631  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.557  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.567061 * X  +   0.041229 * Y  +  -0.822643 * Z  +  51.832645
  Y_new =   0.027660 * X  +  -0.997230 * Y  +  -0.069045 * Z  + -86.464760
  Z_new =  -0.823211 * X  +  -0.061908 * Y  +   0.564350 * Z  +  -4.319098 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.092853  0.967045 -0.109260   [DEG:  177.2074   55.4076   -6.2602 ]
ZXZ: -1.487062  0.971151 -1.645857   [DEG:  -85.2023   55.6429  -94.3007 ]
 
# END of job
