
#######################################################
#                                                     #
#                        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        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       1_F - 46_F        0.99     1.46
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.77     1.45
  LONGEST_CONTINUOUS_SEGMENT:    46       3_F - 48_F        0.93     1.42
  LCS_AVERAGE:     92.09

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     46   49   49      3    7   13   21   37   47   47   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      3   14   34   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      6   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49     17   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49      4   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49     31   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      8   40   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     26   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49     25   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49     16   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     32   41   44   46   46   47   48   48   49   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   46   46   47   48   48   49   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   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      4   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     32   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      6   41   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      3   25   44   46   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     46   49   49      3    4    4    8    9   39   48   48   49   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   10   35   43   48   48   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  97.36  (  92.09  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     41     44     46     46     47     48     48     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  65.31  83.67  89.80  93.88  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
GDT RMS_LOCAL    0.31   0.46   0.56   0.77   0.77   1.01   1.22   1.22   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40
GDT RMS_ALL_AT   1.51   1.52   1.49   1.45   1.45   1.45   1.42   1.42   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40

# 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     5.131     0    0.136   1.061     7.217   31.667   25.357
LGA    G     2_F      G     2_F     3.207     0    0.108   0.108     4.036   48.571   48.571
LGA    K     3_F      K     3_F     1.156     0    0.137   1.070     5.872   83.810   64.180
LGA    I     4_F      I     4_F     0.685     0    0.084   0.109     1.381   90.476   88.214
LGA    K     5_F      K     5_F     0.152     0    0.030   0.994     2.466  100.000   85.238
LGA    R     6_F      R     6_F     0.495     0    0.025   1.534     7.239   97.619   67.879
LGA    F     7_F      F     7_F     0.440     0    0.025   0.087     0.591  100.000   97.403
LGA    F     8_F      F     8_F     0.519     0    0.013   1.313     6.857   95.238   62.468
LGA    A     9_F      A     9_F     0.401     0    0.034   0.043     0.469  100.000  100.000
LGA    K    10_F      K    10_F     0.710     0    0.023   1.067     5.101   95.238   74.656
LGA    D    11_F      D    11_F     0.979     0    0.081   0.954     3.279   90.476   77.798
LGA    M    12_F      M    12_F     0.754     0    0.037   1.135     3.865   92.857   81.429
LGA    R    13_F      R    13_F     0.223     0    0.064   1.566     7.440  100.000   69.524
LGA    A    14_F      A    14_F     0.123     0    0.024   0.029     0.241  100.000  100.000
LGA    A    15_F      A    15_F     0.200     0    0.038   0.035     0.261  100.000  100.000
LGA    L    16_F      L    16_F     0.274     0    0.025   1.100     2.535  100.000   90.238
LGA    A    17_F      A    17_F     0.357     0    0.052   0.059     0.471  100.000  100.000
LGA    Q    18_F      Q    18_F     0.354     0    0.033   0.489     1.823  100.000   93.810
LGA    V    19_F      V    19_F     0.312     0    0.031   0.103     0.504   97.619   98.639
LGA    K    20_F      K    20_F     0.402     0    0.030   0.939     3.317   97.619   87.249
LGA    D    21_F      D    21_F     0.120     0    0.023   0.500     1.308  100.000   96.488
LGA    T    22_F      T    22_F     0.341     0    0.153   1.135     2.269   95.357   87.279
LGA    L    23_F      L    23_F     0.319     0    0.149   1.074     2.789   97.619   88.869
LGA    G    24_F      G    24_F     0.499     0    0.082   0.082     0.987   92.857   92.857
LGA    S    25_F      S    25_F     0.660     0    0.064   0.610     2.605   92.857   86.508
LGA    D    26_F      D    26_F     1.066     0    0.530   1.238     5.088   83.810   69.524
LGA    A    27_F      A    27_F     1.474     0    0.196   0.258     2.011   75.119   76.381
LGA    V    28_F      V    28_F     0.795     0    0.043   0.096     0.897   90.476   90.476
LGA    I    29_F      I    29_F     0.709     0    0.016   0.614     2.924   90.476   86.310
LGA    M    30_F      M    30_F     0.675     0    0.061   0.828     2.620   90.476   85.179
LGA    S    31_F      S    31_F     0.692     0    0.072   0.726     3.522   88.214   81.111
LGA    N    32_F      N    32_F     1.118     0    0.453   0.504     2.626   77.619   79.583
LGA    K    33_F      K    33_F     0.367     0    0.036   0.870     2.749   92.857   82.116
LGA    K    34_F      K    34_F     0.987     0    0.085   0.766     3.098   90.476   78.307
LGA    V    35_F      V    35_F     1.031     0    0.041   1.203     2.996   85.952   77.075
LGA    N    36_F      N    36_F     0.935     0    0.053   1.195     5.657   88.214   67.798
LGA    G    37_F      G    37_F     0.450     0    0.202   0.202     1.140   90.595   90.595
LGA    G    38_F      G    38_F     0.661     0    0.094   0.094     0.661   97.619   97.619
LGA    I    39_F      I    39_F     0.304     0    0.048   0.225     0.802  100.000   97.619
LGA    E    40_F      E    40_F     0.475     0    0.076   0.328     0.857   95.238   94.709
LGA    I    41_F      I    41_F     0.671     0    0.042   1.251     3.329   92.857   83.214
LGA    V    42_F      V    42_F     0.351     0    0.032   1.343     3.046  100.000   86.735
LGA    A    43_F      A    43_F     0.596     0    0.056   0.064     0.734   92.857   92.381
LGA    A    44_F      A    44_F     0.702     0    0.027   0.024     0.918   90.476   90.476
LGA    V    45_F      V    45_F     0.587     0    0.053   1.256     3.536   90.476   80.068
LGA    L    46_F      L    46_F     0.803     0    0.624   1.127     4.263   78.095   63.690
LGA    E    47_F      E    47_F     1.975     0    0.268   0.819     6.107   60.000   48.624
LGA    H    48_F      H    48_F     4.240     0    0.268   1.063    12.690   43.690   19.095
LGA    H    49_F      H    49_F     4.512     0    0.192   1.212     7.023   26.548   26.429

# 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):     1.398          1.477                  2.544           88.000   79.791

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     48    1.22    93.878    96.643     3.626

LGA_LOCAL      RMSD:   1.224  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.416  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.398  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.797407 * X  +  -0.305649 * Y  +   0.520308 * Z  +  54.889019
  Y_new =   0.242141 * X  +   0.951843 * Y  +   0.188053 * Z  + -74.846718
  Z_new =  -0.552729 * X  +  -0.023967 * Y  +   0.833016 * Z  +  -2.823944 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.294811  0.585636 -0.028763   [DEG:   16.8914   33.5545   -1.6480 ]
ZXZ:  1.917613  0.586259 -1.614130   [DEG:  109.8711   33.5902  -92.4828 ]
 
# END of job
