
#######################################################
#                                                     #
#                        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   45 (  360),  selected   45 , name one
# Molecule2: number of CA atoms  153 ( 1242),  selected   45 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      17_C - 37_C        4.96    18.04
  LCS_AVERAGE:     11.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      27_C - 40_C        1.93    17.58
  LONGEST_CONTINUOUS_SEGMENT:    14      28_C - 41_C        1.92    18.13
  LCS_AVERAGE:      5.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      28_C - 40_C        1.00    17.71
  LCS_AVERAGE:      4.85

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     H     2_C     H     2_C      9    9   15      4    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     C     3_C     C     3_C      9    9   15      4    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     P     4_C     P     4_C      9    9   15      5    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     F     5_C     F     5_C      9    9   15      5    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     C     6_C     C     6_C      9    9   15      5    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     F     7_C     F     7_C      9    9   15      3    6    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     A     8_C     A     8_C      9    9   15      5    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     V     9_C     V     9_C      9    9   15      5    7    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   21 
LCS_GDT     D    10_C     D    10_C      9    9   15      3    5    9   10   11   11   12   12   12   13   13   14   14   15   16   17   18   21   21   22 
LCS_GDT     T    11_C     T    11_C      4    5   15      3    4    4    4    5    6   10   12   12   13   13   14   14   15   17   19   20   21   23   23 
LCS_GDT     K    12_C     K    12_C      4    5   15      3    4    4   10   11   11   12   12   12   13   13   14   14   15   17   19   20   21   23   25 
LCS_GDT     V    13_C     V    13_C      4    4   15      3    4    9   10   11   11   12   12   12   13   13   14   14   15   17   19   20   21   23   25 
LCS_GDT     I    14_C     I    14_C      4    4   15      3    4    4    8   10   11   12   12   12   13   13   14   14   15   18   20   23   24   25   26 
LCS_GDT     D    15_C     D    15_C      3    4   15      3    3    3    4    4    4    6    7   10   12   13   14   15   17   18   21   23   25   25   26 
LCS_GDT     S    16_C     S    16_C      3    4   19      1    3    3    4    4    5    6    7   10   12   12   14   17   20   21   22   24   25   25   27 
LCS_GDT     R    17_C     R    17_C      3    3   21      3    3    3    3   11   15   15   16   16   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     L    18_C     L    18_C      3    4   21      3    3    3    4    5    9   14   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     V    19_C     V    19_C      3    4   21      3    3    3    5   11   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     G    20_C     G    20_C      3    6   21      3    4    6    6    7    8   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     E    21_C     E    21_C      3    6   21      3    3    3    4    5    5    6    7   10   12   12   13   14   21   23   24   25   26   27   27 
LCS_GDT     G    22_C     G    22_C      4    6   21      3    4    6    6    7    8    9   10   13   15   16   16   19   20   23   24   25   26   27   27 
LCS_GDT     S    23_C     S    23_C      4    6   21      3    4    6    6    7    9   11   13   14   15   16   18   19   21   22   24   25   26   27   27 
LCS_GDT     S    24_C     S    24_C      4    8   21      3    4    6    6    8   10   11   13   14   15   16   18   19   21   22   23   25   26   27   27 
LCS_GDT     V    25_C     V    25_C      5    8   21      3    4    6    6    8   10   11   13   14   15   16   18   19   21   22   24   25   26   27   27 
LCS_GDT     R    26_C     R    26_C      5    8   21      3    4    6    6    8   10   11   15   16   17   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     R    27_C     R    27_C      5   14   21      3    4    5    6    8   10   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     R    28_C     R    28_C     13   14   21      4    8   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     R    29_C     R    29_C     13   14   21      6   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     Q    30_C     Q    30_C     13   14   21      6   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     C    31_C     C    31_C     13   14   21      6   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     L    32_C     L    32_C     13   14   21      6   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     V    33_C     V    33_C     13   14   21      6   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     C    34_C     C    34_C     13   14   21      6    8   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     N    35_C     N    35_C     13   14   21      4    5   10   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     E    36_C     E    36_C     13   14   21      4   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     R    37_C     R    37_C     13   14   21      3   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     F    38_C     F    38_C     13   14   20      4   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     T    39_C     T    39_C     13   14   20      5   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     T    40_C     T    40_C     13   14   20      3   10   12   13   13   15   15   16   17   18   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     F    41_C     F    41_C      4   14   20      3    3    5    5    5    5    6   11   14   15   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     E    42_C     E    42_C      4    4   19      3    3    5    5    5    5   10   14   16   16   18   19   21   21   23   24   25   26   27   27 
LCS_GDT     V    43_C     V    43_C      3    3   18      3    3    3    4    4    5    6    7   10   12   12   13   14   20   23   24   25   26   27   27 
LCS_GDT     A    44_C     A    44_C      3    3    8      3    3    3    4    4    5    6    7   10   12   12   13   14   15   17   19   20   21   23   25 
LCS_GDT     E    45_C     E    45_C      3    3    8      3    3    3    4    4    5    6    7   10   12   12   13   14   15   17   19   20   21   23   25 
LCS_GDT     L    46_C     L    46_C      3    3    8      3    3    3    3    3    4    4    7   10   11   12   13   14   15   17   19   20   21   23   25 
LCS_AVERAGE  LCS_A:   7.44  (   4.85    5.69   11.78 )

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      6     10     12     13     13     15     15     16     17     18     18     19     21     21     23     24     25     26     27     27 
GDT PERCENT_AT   3.92   6.54   7.84   8.50   8.50   9.80   9.80  10.46  11.11  11.76  11.76  12.42  13.73  13.73  15.03  15.69  16.34  16.99  17.65  17.65
GDT RMS_LOCAL    0.30   0.60   0.82   1.00   1.00   1.94   1.94   2.20   2.81   2.92   2.92   3.29   3.82   3.82   4.79   5.36   5.46   5.70   5.95   5.95
GDT RMS_ALL_AT  17.03  17.65  17.65  17.71  17.71  17.43  17.43  17.44  17.37  17.29  17.29  17.44  17.66  17.66  17.85  17.78  17.62  17.54  17.71  17.71

# Checking swapping
#   possible swapping detected:  E    45_C      E    45_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H     2_C      H     2_C    29.467     0    0.707   1.242    30.584    0.000    0.000
LGA    C     3_C      C     3_C    28.729     0    0.189   0.280    32.470    0.000    0.000
LGA    P     4_C      P     4_C    31.459     0    0.039   0.055    33.741    0.000    0.000
LGA    F     5_C      F     5_C    31.477     0    0.092   1.414    34.892    0.000    0.000
LGA    C     6_C      C     6_C    33.700     0    0.689   0.597    36.420    0.000    0.000
LGA    F     7_C      F     7_C    35.254     0    0.094   0.289    38.664    0.000    0.000
LGA    A     8_C      A     8_C    32.804     0    0.044   0.054    33.161    0.000    0.000
LGA    V     9_C      V     9_C    32.355     0    0.600   0.919    35.883    0.000    0.000
LGA    D    10_C      D    10_C    29.145     0    0.228   0.796    30.526    0.000    0.000
LGA    T    11_C      T    11_C    26.785     0    0.630   0.901    27.068    0.000    0.000
LGA    K    12_C      K    12_C    22.749     0    0.047   0.577    26.992    0.000    0.000
LGA    V    13_C      V    13_C    17.486     0    0.634   0.661    19.471    0.000    0.000
LGA    I    14_C      I    14_C    14.423     0    0.017   0.241    17.583    0.000    0.000
LGA    D    15_C      D    15_C    12.947     0    0.546   0.684    16.058    0.000    0.000
LGA    S    16_C      S    16_C     9.690     0    0.536   0.780    11.207    4.405    3.016
LGA    R    17_C      R    17_C     2.803     0    0.606   1.073    11.645   59.405   30.260
LGA    L    18_C      L    18_C     4.286     0    0.603   0.789     8.190   35.714   23.988
LGA    V    19_C      V    19_C     2.998     0    0.567   0.739     6.730   39.762   48.435
LGA    G    20_C      G    20_C     7.600     0    0.305   0.305    12.019    9.762    9.762
LGA    E    21_C      E    21_C    12.433     0    0.450   0.676    16.111    0.119    0.053
LGA    G    22_C      G    22_C    13.287     0    0.179   0.179    16.187    0.000    0.000
LGA    S    23_C      S    23_C    15.227     0    0.119   0.589    18.046    0.000    0.000
LGA    S    24_C      S    24_C    15.217     0    0.635   0.779    15.373    0.000    0.000
LGA    V    25_C      V    25_C    13.606     0    0.555   0.633    17.781    0.000    0.000
LGA    R    26_C      R    26_C     8.695     0    0.103   1.236    10.805    8.690    4.978
LGA    R    27_C      R    27_C     6.149     0    0.251   0.876    17.750   18.929    7.316
LGA    R    28_C      R    28_C     2.923     0    0.654   1.128    11.162   59.048   31.212
LGA    R    29_C      R    29_C     1.514     0    0.197   1.142     4.996   77.143   62.684
LGA    Q    30_C      Q    30_C     0.745     0    0.014   0.618     1.821   90.595   82.646
LGA    C    31_C      C    31_C     0.661     0    0.035   0.061     1.562   92.857   89.127
LGA    L    32_C      L    32_C     1.331     0    0.212   0.232     2.308   75.119   77.202
LGA    V    33_C      V    33_C     1.557     0    0.129   0.356     3.517   77.143   69.932
LGA    C    34_C      C    34_C     1.092     0    0.702   0.616     2.531   75.357   77.381
LGA    N    35_C      N    35_C     2.581     0    0.060   1.211     7.657   62.976   41.190
LGA    E    36_C      E    36_C     1.253     0    0.074   0.628     3.415   88.333   74.656
LGA    R    37_C      R    37_C     1.257     0    0.029   0.808     3.402   77.143   74.199
LGA    F    38_C      F    38_C     2.019     0    0.055   1.192     3.642   66.786   68.788
LGA    T    39_C      T    39_C     2.561     0    0.656   0.921     5.393   49.524   54.966
LGA    T    40_C      T    40_C     2.107     0    0.118   0.470     5.142   51.786   57.619
LGA    F    41_C      F    41_C     7.255     0    0.577   1.360    15.986   12.738    4.762
LGA    E    42_C      E    42_C     7.373     0    0.595   0.602    11.890    6.905    5.079
LGA    V    43_C      V    43_C    12.577     0    0.657   0.650    15.340    0.000    0.000
LGA    A    44_C      A    44_C    18.265     0    0.659   0.605    20.601    0.000    0.000
LGA    E    45_C      E    45_C    18.410     0    0.616   0.823    21.346    0.000    0.000
LGA    L    46_C      L    46_C    22.106     0    0.666   0.523    26.014    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     360    360  100.00               153
SUMMARY(RMSD_GDC):    15.680         15.841                 15.666            7.453    6.531

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45  153    4.0     16    2.20    10.294     9.172     0.696

LGA_LOCAL      RMSD:   2.198  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.442  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:  15.680  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.846874 * X  +  -0.433873 * Y  +  -0.307505 * Z  + -27.340664
  Y_new =  -0.187354 * X  +   0.297748 * Y  +  -0.936080 * Z  +  11.052672
  Z_new =   0.497698 * X  +   0.850353 * Y  +   0.170867 * Z  +   7.327981 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.217723 -0.520943  1.372500   [DEG:  -12.4746  -29.8478   78.6385 ]
ZXZ: -0.317397  1.399086  0.529529   [DEG:  -18.1855   80.1618   30.3398 ]
 
# END of job
