
#######################################################
#                                                     #
#                        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        2.63     2.63
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        1.72     2.77
  LONGEST_CONTINUOUS_SEGMENT:    46       3_F - 48_F        1.88     2.76
  LCS_AVERAGE:     91.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       4_F - 25_F        0.99     3.14
  LONGEST_CONTINUOUS_SEGMENT:    22       6_F - 27_F        0.97     3.69
  LCS_AVERAGE:     40.36

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   20   49      3    3    6    8   12   15   21   28   35   39   46   47   48   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     12   46   49      3    7   12   20   28   39   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     15   46   49      3   19   23   27   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     22   46   49      7   21   32   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     22   46   49     10   21   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     22   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     22   46   49     11   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     22   46   49      8   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     22   46   49      8   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     22   46   49     11   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     22   46   49      8   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     22   46   49      5   20   34   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     22   46   49      5   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     22   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     22   46   49      8   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     22   46   49      5   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     22   46   49      4   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     22   46   49      3    8   28   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     22   46   49      3   11   20   30   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     22   46   49      8   19   29   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     21   46   49      8   19   32   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     21   46   49      8   19   33   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     21   46   49      8   19   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     21   46   49      3   19   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     21   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     21   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     21   46   49      6   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     21   46   49      9   19   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     21   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     21   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     21   46   49     10   19   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     21   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     21   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     21   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     21   46   49      8   22   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     21   46   49     12   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     21   46   49     10   23   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     21   46   49      3   19   32   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     21   46   49      3    5   35   41   42   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F      4   46   49      3   11   21   33   40   44   44   45   46   46   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F      4   46   49      3    3    4    5    7   10   22   41   42   45   47   47   48   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3    5   49      0    3    3    5    5    5    9   13   21   23   38   47   48   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  77.15  (  40.36   91.09  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     12     23     35     41     42     44     44     45     46     46     47     47     48     49     49     49     49     49     49     49 
GDT PERCENT_AT  24.49  46.94  71.43  83.67  85.71  89.80  89.80  91.84  93.88  93.88  95.92  95.92  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.65   1.00   1.19   1.23   1.41   1.41   1.52   1.72   1.72   2.03   2.03   2.36   2.63   2.63   2.63   2.63   2.63   2.63   2.63
GDT RMS_ALL_AT   3.15   2.94   2.88   2.93   2.93   2.92   2.92   2.85   2.77   2.77   2.71   2.71   2.66   2.63   2.63   2.63   2.63   2.63   2.63   2.63

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    11_F      D    11_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     9.987     0    0.288   1.133    12.887    3.095    1.548
LGA    G     2_F      G     2_F     5.916     0    0.200   0.200     7.517   17.976   17.976
LGA    K     3_F      K     3_F     3.464     0    0.208   0.975     6.206   54.167   39.418
LGA    I     4_F      I     4_F     1.621     0    0.103   0.995     4.103   75.119   66.667
LGA    K     5_F      K     5_F     0.865     0    0.013   0.690     2.886   88.214   76.402
LGA    R     6_F      R     6_F     0.510     0    0.051   0.998     4.450   90.476   71.645
LGA    F     7_F      F     7_F     0.316     0    0.045   1.139     5.236  100.000   73.896
LGA    F     8_F      F     8_F     0.437     0    0.020   0.724     2.600   97.619   86.147
LGA    A     9_F      A     9_F     0.412     0    0.079   0.100     0.871   97.619   96.190
LGA    K    10_F      K    10_F     0.650     0    0.059   1.237     5.604   92.857   73.704
LGA    D    11_F      D    11_F     1.154     0    0.053   0.869     3.286   88.214   76.667
LGA    M    12_F      M    12_F     0.998     0    0.048   1.243     4.482   88.214   73.452
LGA    R    13_F      R    13_F     1.157     0    0.035   1.819     9.538   81.429   47.662
LGA    A    14_F      A    14_F     1.296     0    0.037   0.046     1.379   81.429   81.429
LGA    A    15_F      A    15_F     0.960     0    0.073   0.078     1.097   88.214   86.857
LGA    L    16_F      L    16_F     0.872     0    0.038   0.749     2.993   88.214   78.810
LGA    A    17_F      A    17_F     1.458     0    0.053   0.050     1.818   77.143   76.286
LGA    Q    18_F      Q    18_F     1.897     0    0.019   0.573     2.146   70.833   75.873
LGA    V    19_F      V    19_F     1.240     0    0.086   0.993     3.654   85.952   77.347
LGA    K    20_F      K    20_F     0.518     0    0.049   1.137     6.275   92.857   71.958
LGA    D    21_F      D    21_F     1.139     0    0.046   0.883     5.083   81.429   65.595
LGA    T    22_F      T    22_F     1.277     0    0.117   0.165     1.546   79.286   80.204
LGA    L    23_F      L    23_F     1.560     0    0.043   0.508     2.084   75.000   72.917
LGA    G    24_F      G    24_F     1.264     0    0.026   0.026     1.418   81.429   81.429
LGA    S    25_F      S    25_F     2.190     0    0.076   0.600     3.196   61.190   63.889
LGA    D    26_F      D    26_F     3.454     0    0.623   1.146     7.347   57.262   39.167
LGA    A    27_F      A    27_F     2.258     0    0.136   0.172     2.932   60.952   61.714
LGA    V    28_F      V    28_F     1.971     0    0.082   0.161     2.559   75.000   69.524
LGA    I    29_F      I    29_F     1.717     0    0.034   1.087     4.203   70.833   68.512
LGA    M    30_F      M    30_F     1.770     0    0.061   0.884     2.654   71.071   70.000
LGA    S    31_F      S    31_F     1.488     0    0.112   0.238     2.293   83.690   77.381
LGA    N    32_F      N    32_F     0.733     0    0.260   0.762     4.441   95.238   73.929
LGA    K    33_F      K    33_F     0.320     0    0.044   0.858     4.545   90.595   70.159
LGA    K    34_F      K    34_F     1.232     0    0.061   0.767     4.604   83.690   64.974
LGA    V    35_F      V    35_F     1.341     0    0.282   1.020     4.160   73.214   65.714
LGA    N    36_F      N    36_F     0.926     0    0.215   1.371     4.516   85.952   70.476
LGA    G    37_F      G    37_F     0.869     0    0.213   0.213     0.869   92.857   92.857
LGA    G    38_F      G    38_F     1.435     0    0.127   0.127     2.178   77.262   77.262
LGA    I    39_F      I    39_F     0.663     0    0.122   0.409     1.257   90.476   89.345
LGA    E    40_F      E    40_F     0.616     0    0.083   0.737     2.840   95.238   81.217
LGA    I    41_F      I    41_F     0.556     0    0.048   1.143     2.707   90.476   81.905
LGA    V    42_F      V    42_F     1.048     0    0.260   1.172     3.031   90.595   79.728
LGA    A    43_F      A    43_F     0.556     0    0.123   0.150     0.975   92.857   92.381
LGA    A    44_F      A    44_F     0.840     0    0.022   0.024     1.122   88.214   88.667
LGA    V    45_F      V    45_F     1.766     0    0.206   0.188     4.325   83.810   66.531
LGA    L    46_F      L    46_F     1.703     0    0.563   1.469     7.222   62.143   45.417
LGA    E    47_F      E    47_F     3.830     0    0.415   0.723     8.090   32.262   23.862
LGA    H    48_F      H    48_F     8.136     0    0.479   1.168    13.323    8.929    3.762
LGA    H    49_F      H    49_F     9.641     0    0.562   0.683    17.038    3.810    1.524

# 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):     2.635          2.588                  3.686           75.396   66.734

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     45    1.52    80.612    86.798     2.782

LGA_LOCAL      RMSD:   1.517  Number of atoms:   45  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.848  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   2.635  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.435986 * X  +   0.270290 * Y  +   0.858406 * Z  +  53.983109
  Y_new =  -0.251955 * X  +  -0.952349 * Y  +   0.171902 * Z  + -80.788063
  Z_new =   0.863965 * X  +  -0.141333 * Y  +   0.483311 * Z  +  -7.834774 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.617584 -1.043091 -0.284494   [DEG: -149.9765  -59.7647  -16.3003 ]
ZXZ:  1.768439  1.066363  1.732946   [DEG:  101.3241   61.0981   99.2905 ]
 
# END of job
