
#######################################################
#                                                     #
#                        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        1.82     1.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.82     1.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       3_F - 48_F        0.93     1.85
  LCS_AVERAGE:     90.46

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      4   49   49      3    4    7   12   16   20   32   39   46   47   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     44   49   49      4   11   27   41   45   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      4   13   26   44   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     12   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     13   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     14   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49      5   34   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     19   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     19   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49      4   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49     18   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49      4   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      7   35   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     10   36   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     16   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     10   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49     13   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      4   12   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49      4   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      3   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     20   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     21   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     14   37   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     14   32   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      6   34   43   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      3   13   42   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     46   49   49      3    7   41   45   46   47   47   47   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      8   49   49      3    5    9   12   16   31   40   43   48   48   48   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  96.82  (  90.46  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     21     37     43     45     46     47     47     47     48     48     48     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  42.86  75.51  87.76  91.84  93.88  95.92  95.92  95.92  97.96  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.61   0.74   0.84   0.93   1.08   1.08   1.08   1.40   1.40   1.40   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82
GDT RMS_ALL_AT   1.93   1.86   1.88   1.88   1.85   1.83   1.83   1.83   1.86   1.86   1.86   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82

# Checking swapping
#   possible swapping detected:  F     8_F      F     8_F
#   possible swapping detected:  D    11_F      D    11_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F     8.093     0    0.480   0.824     9.052    4.762    8.750
LGA    G     2_F      G     2_F     3.683     0    0.012   0.012     4.672   40.476   40.476
LGA    K     3_F      K     3_F     2.531     0    0.034   1.071     6.547   65.000   47.566
LGA    I     4_F      I     4_F     0.920     0    0.088   0.152     1.376   90.595   88.274
LGA    K     5_F      K     5_F     0.656     0    0.037   0.952     3.712   92.857   71.058
LGA    R     6_F      R     6_F     0.377     0    0.046   0.852     4.264  100.000   85.325
LGA    F     7_F      F     7_F     0.432     0    0.021   0.063     0.488  100.000  100.000
LGA    F     8_F      F     8_F     0.537     0    0.030   1.296     6.906   90.476   60.736
LGA    A     9_F      A     9_F     0.393     0    0.071   0.088     0.855   95.238   96.190
LGA    K    10_F      K    10_F     0.785     0    0.039   1.019     5.778   95.238   72.540
LGA    D    11_F      D    11_F     1.247     0    0.093   0.961     3.569   90.595   77.024
LGA    M    12_F      M    12_F     0.625     0    0.068   1.038     4.302   95.238   82.976
LGA    R    13_F      R    13_F     0.592     0    0.061   1.921    10.438   92.857   51.861
LGA    A    14_F      A    14_F     0.614     0    0.034   0.037     0.686   90.476   90.476
LGA    A    15_F      A    15_F     0.444     0    0.047   0.047     0.489  100.000  100.000
LGA    L    16_F      L    16_F     0.323     0    0.011   1.108     2.976  100.000   88.869
LGA    A    17_F      A    17_F     0.798     0    0.033   0.035     0.984   90.476   90.476
LGA    Q    18_F      Q    18_F     0.825     0    0.022   0.354     1.204   90.476   90.529
LGA    V    19_F      V    19_F     0.459     0    0.018   0.076     0.489  100.000  100.000
LGA    K    20_F      K    20_F     0.384     0    0.041   1.457     7.584  100.000   68.042
LGA    D    21_F      D    21_F     0.793     0    0.019   0.825     4.110   90.476   71.726
LGA    T    22_F      T    22_F     0.900     0    0.105   1.101     2.599   88.214   83.129
LGA    L    23_F      L    23_F     0.874     0    0.114   1.123     3.401   90.476   83.155
LGA    G    24_F      G    24_F     0.802     0    0.123   0.123     1.171   88.214   88.214
LGA    S    25_F      S    25_F     0.374     0    0.083   0.091     0.883   95.238   96.825
LGA    D    26_F      D    26_F     1.058     0    0.551   0.741     3.893   86.190   70.179
LGA    A    27_F      A    27_F     1.453     0    0.120   0.175     1.869   77.143   78.000
LGA    V    28_F      V    28_F     1.155     0    0.049   0.065     1.480   85.952   84.014
LGA    I    29_F      I    29_F     0.780     0    0.067   0.658     2.791   88.214   85.179
LGA    M    30_F      M    30_F     0.734     0    0.022   0.138     0.899   90.476   94.048
LGA    S    31_F      S    31_F     0.647     0    0.071   0.502     2.764   92.857   85.000
LGA    N    32_F      N    32_F     0.660     0    0.383   1.226     4.459   86.429   75.357
LGA    K    33_F      K    33_F     0.702     0    0.067   1.296     6.386   88.214   66.667
LGA    K    34_F      K    34_F     1.281     0    0.127   0.755     3.447   81.548   68.995
LGA    V    35_F      V    35_F     0.972     0    0.051   1.186     2.745   85.952   79.456
LGA    N    36_F      N    36_F     0.835     0    0.239   1.231     4.935   83.810   70.536
LGA    G    37_F      G    37_F     0.574     0    0.203   0.203     0.814   95.238   95.238
LGA    G    38_F      G    38_F     0.257     0    0.071   0.071     0.321  100.000  100.000
LGA    I    39_F      I    39_F     0.246     0    0.071   1.019     2.481  100.000   87.798
LGA    E    40_F      E    40_F     0.333     0    0.059   0.178     0.840   95.238   97.884
LGA    I    41_F      I    41_F     0.619     0    0.059   1.257     3.014   92.857   82.202
LGA    V    42_F      V    42_F     0.184     0    0.024   1.173     2.639   97.619   86.122
LGA    A    43_F      A    43_F     0.236     0    0.082   0.105     0.562  100.000   98.095
LGA    A    44_F      A    44_F     0.415     0    0.034   0.031     1.101   92.976   92.476
LGA    V    45_F      V    45_F     1.484     0    0.025   0.932     3.712   88.214   74.014
LGA    L    46_F      L    46_F     1.595     0    0.608   1.201     4.743   69.286   55.952
LGA    E    47_F      E    47_F     1.754     0    0.123   0.648     7.030   83.810   52.804
LGA    H    48_F      H    48_F     2.248     0    0.056   1.093     8.511   57.500   32.000
LGA    H    49_F      H    49_F     6.680     0    0.661   1.246    10.166   12.381    5.810

# 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):     1.819          1.968                  2.940           85.904   76.572

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     47    1.08    90.816    95.211     3.987

LGA_LOCAL      RMSD:   1.079  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.834  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.819  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.128678 * X  +  -0.861672 * Y  +   0.490881 * Z  +  66.188324
  Y_new =  -0.091651 * X  +  -0.503210 * Y  +  -0.859290 * Z  + -77.593300
  Z_new =   0.987442 * X  +   0.065582 * Y  +  -0.143725 * Z  + -19.236860 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.618901 -1.412151  2.713511   [DEG:  -35.4604  -80.9103  155.4727 ]
ZXZ:  0.519021  1.715021  1.504478   [DEG:   29.7377   98.2635   86.2002 ]
 
# END of job
