
#######################################################
#                                                     #
#                        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        1.19     1.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.19     1.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48       2_F - 49_F        0.94     1.21
  LCS_AVERAGE:     96.17

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      5   49   49      3    6   11   16   24   44   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     48   49   49      3   13   35   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     48   49   49      6   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     48   49   49      5   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     48   49   49     20   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     48   49   49      8   40   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     48   49   49     27   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     48   49   49      8   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     48   49   49      9   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     48   49   49      4    6   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     48   49   49      4   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     48   49   49     27   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     48   49   49     30   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     48   49   49     32   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     48   49   49     16   42   45   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     48   49   49      3   14   39   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     48   49   49      3    3    3   13   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F     48   49   49      0   40   45   45   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  98.72  (  96.17  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     32     42     45     46     47     48     48     49     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  65.31  85.71  91.84  93.88  95.92  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.52   0.60   0.79   0.83   0.94   0.94   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19
GDT RMS_ALL_AT   1.29   1.27   1.31   1.21   1.23   1.21   1.21   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  D    21_F      D    21_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     4.965     0    0.115   0.909     7.492   34.286   24.405
LGA    G     2_F      G     2_F     2.503     0    0.120   0.120     3.553   57.619   57.619
LGA    K     3_F      K     3_F     0.713     0    0.169   1.059     5.782   88.214   69.418
LGA    I     4_F      I     4_F     0.608     0    0.081   0.126     1.230   88.214   87.083
LGA    K     5_F      K     5_F     0.452     0    0.033   0.983     3.394  100.000   81.640
LGA    R     6_F      R     6_F     0.772     0    0.014   1.276     6.139   90.476   75.238
LGA    F     7_F      F     7_F     0.640     0    0.013   0.076     0.723   90.476   91.342
LGA    F     8_F      F     8_F     0.557     0    0.011   1.289     6.926   90.476   61.299
LGA    A     9_F      A     9_F     0.397     0    0.040   0.059     0.479  100.000  100.000
LGA    K    10_F      K    10_F     0.431     0    0.029   1.046     4.970   97.619   79.206
LGA    D    11_F      D    11_F     1.092     0    0.087   1.003     3.159   90.595   78.869
LGA    M    12_F      M    12_F     0.386     0    0.013   1.419     4.987   97.619   82.500
LGA    R    13_F      R    13_F     0.475     0    0.060   1.565     8.039   97.619   62.814
LGA    A    14_F      A    14_F     0.431     0    0.018   0.035     0.488  100.000  100.000
LGA    A    15_F      A    15_F     0.418     0    0.058   0.069     0.501  100.000   98.095
LGA    L    16_F      L    16_F     0.303     0    0.018   1.101     2.335  100.000   90.000
LGA    A    17_F      A    17_F     0.699     0    0.049   0.055     0.812   90.476   90.476
LGA    Q    18_F      Q    18_F     0.773     0    0.035   0.173     1.136   90.476   89.471
LGA    V    19_F      V    19_F     0.547     0    0.038   0.081     0.581   92.857   95.918
LGA    K    20_F      K    20_F     0.290     0    0.028   0.962     4.039  100.000   85.026
LGA    D    21_F      D    21_F     0.497     0    0.017   0.544     1.716   97.619   91.845
LGA    T    22_F      T    22_F     0.603     0    0.169   1.125     2.375   92.857   85.646
LGA    L    23_F      L    23_F     0.630     0    0.160   1.112     2.860   90.476   84.107
LGA    G    24_F      G    24_F     0.657     0    0.055   0.055     0.871   95.238   95.238
LGA    S    25_F      S    25_F     0.299     0    0.043   0.168     0.631  100.000   96.825
LGA    D    26_F      D    26_F     0.725     0    0.499   0.942     4.582   92.976   73.155
LGA    A    27_F      A    27_F     1.454     0    0.205   0.269     2.000   75.119   76.381
LGA    V    28_F      V    28_F     0.971     0    0.038   0.084     1.124   90.476   87.891
LGA    I    29_F      I    29_F     0.739     0    0.012   0.626     2.844   90.476   86.310
LGA    M    30_F      M    30_F     0.850     0    0.033   0.640     3.274   88.214   84.286
LGA    S    31_F      S    31_F     0.742     0    0.036   0.580     2.576   90.476   83.413
LGA    N    32_F      N    32_F     1.127     0    0.464   0.436     2.865   77.619   80.714
LGA    K    33_F      K    33_F     0.537     0    0.073   0.922     3.394   88.214   76.455
LGA    K    34_F      K    34_F     1.177     0    0.092   0.758     3.222   83.690   72.487
LGA    V    35_F      V    35_F     1.011     0    0.039   1.198     3.185   85.952   78.435
LGA    N    36_F      N    36_F     0.561     0    0.070   1.143     5.045   92.857   72.679
LGA    G    37_F      G    37_F     0.354     0    0.214   0.214     0.882   97.619   97.619
LGA    G    38_F      G    38_F     0.602     0    0.092   0.092     0.623   95.238   95.238
LGA    I    39_F      I    39_F     0.310     0    0.073   1.272     3.060   97.619   81.845
LGA    E    40_F      E    40_F     0.490     0    0.096   0.498     1.611   92.976   88.624
LGA    I    41_F      I    41_F     0.815     0    0.036   1.230     3.470   90.476   82.024
LGA    V    42_F      V    42_F     0.390     0    0.025   1.156     2.748   95.238   86.122
LGA    A    43_F      A    43_F     0.654     0    0.058   0.065     0.796   92.857   92.381
LGA    A    44_F      A    44_F     0.821     0    0.030   0.040     1.014   90.476   88.667
LGA    V    45_F      V    45_F     0.544     0    0.023   0.977     2.879   95.238   85.918
LGA    L    46_F      L    46_F     0.612     0    0.606   1.100     4.006   80.476   67.619
LGA    E    47_F      E    47_F     1.886     0    0.350   0.831     5.381   65.595   53.598
LGA    H    48_F      H    48_F     2.834     0    0.298   0.978    10.920   65.000   29.286
LGA    H    49_F      H    49_F     2.438     0    0.171   0.977     5.297   58.929   51.000

# 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):     1.189          1.252                  2.366           88.715   80.127

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     49    1.19    94.898    97.324     3.801

LGA_LOCAL      RMSD:   1.189  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.189  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.189  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.565967 * X  +  -0.780732 * Y  +  -0.264837 * Z  +  53.405033
  Y_new =   0.802606 * X  +   0.448364 * Y  +   0.393437 * Z  + -78.217850
  Z_new =  -0.188425 * X  +  -0.435232 * Y  +   0.880380 * Z  +  -3.242777 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.956615  0.189559 -0.459132   [DEG:   54.8100   10.8609  -26.3063 ]
ZXZ: -2.549124  0.494133 -2.733023   [DEG: -146.0541   28.3118 -156.5907 ]
 
# END of job
