
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      10_A - 34_A        4.93     7.30
  LONGEST_CONTINUOUS_SEGMENT:    25      11_A - 35_A        4.65     7.53
  LCS_AVERAGE:     64.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      17_A - 29_A        1.84    10.28
  LCS_AVERAGE:     27.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      24_A - 32_A        0.69     7.66
  LCS_AVERAGE:     17.71

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     S     1_A     S     1_A      3    3   13      0    3    3    3    3    4    4    7    8    9   11   21   24   25   26   26   28   30   33   33 
LCS_GDT     D     2_A     D     2_A      3    3   13      3    3    3    3    3    5    5    7    8    9   11   14   24   25   26   26   28   30   33   33 
LCS_GDT     E     3_A     E     3_A      3    3   13      3    3    3    3    3    5    6    7    9    9   11   14   17   20   20   25   27   29   33   33 
LCS_GDT     M     4_A     M     4_A      3    3   13      3    3    3    3    4    5    7    8   11   11   13   16   19   21   24   26   28   30   33   33 
LCS_GDT     W     5_A     W     5_A      3    3   18      3    3    3    4    4    5    7    8    9    9   11   12   17   17   21   25   27   30   33   33 
LCS_GDT     F     6_A     F     6_A      3    3   19      3    3    3    4    4    4    7    8   11   11   14   15   19   21   23   26   28   30   33   33 
LCS_GDT     C     7_A     C     7_A      5    5   19      4    5    5    5    5    5    7   10   12   13   14   16   19   21   22   24   28   30   33   33 
LCS_GDT     E     8_A     E     8_A      5    5   19      4    5    5    5    5    9   10   11   12   13   15   17   17   19   22   23   26   28   30   31 
LCS_GDT     T     9_A     T     9_A      5    5   19      4    5    5    5    5    5    7    8    9   12   14   15   19   21   22   23   26   26   28   30 
LCS_GDT     L    10_A     L    10_A      5    5   25      4    5    5    5    5    9   10   11   12   14   15   18   20   21   23   26   28   30   33   33 
LCS_GDT     R    11_A     R    11_A      5    5   25      4    5    5    5    5    5    6    8    9   13   15   18   19   21   23   25   28   30   33   33 
LCS_GDT     R    12_A     R    12_A      3    4   25      3    3    3    3    4    5    9   13   14   15   16   18   20   23   26   26   28   30   33   33 
LCS_GDT     L    13_A     L    13_A      3    9   25      3    9   10   12   13   13   17   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     L    14_A     L    14_A      6   12   25      3    3    7   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     C    15_A     C    15_A      8   12   25      0    5    8    9   11   11   14   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     P    16_A     P    16_A      8   12   25      4    5    8   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     K    17_A     K    17_A      8   13   25      4    5    8   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     S    18_A     S    18_A      8   13   25      5    5    8   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     C    19_A     C    19_A      8   13   25      5    5    8   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     S    20_A     S    20_A      8   13   25      5    5    8   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     I    21_A     I    21_A      8   13   25      5    5    8   10   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     E    22_A     E    22_A      8   13   25      5    5    8   11   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     G    23_A     G    23_A      6   13   25      3    5    8   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     G    24_A     G    24_A      9   13   25      4    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     C    25_A     C    25_A      9   13   25      4    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     P    26_A     P    26_A      9   13   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     E    27_A     E    27_A      9   13   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     V    28_A     V    28_A      9   13   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     C    29_A     C    29_A      9   13   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     S    30_A     S    30_A      9   12   25      6    8   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     H    31_A     H    31_A      9   12   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     M    32_A     M    32_A      9   12   25      6    9   10   12   13   16   18   19   19   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     C    33_A     C    33_A      4   12   25      3    3    6   10   11   12   13   14   17   21   21   22   24   25   26   26   28   30   33   33 
LCS_GDT     P    34_A     P    34_A      4   12   25      3    3    6   10   11   12   13   13   15   18   19   22   24   25   26   26   28   30   33   33 
LCS_GDT     L    35_A     L    35_A      3   12   25      0    3    6   10   11   12   13   14   15   18   19   21   24   25   26   26   28   30   33   33 
LCS_AVERAGE  LCS_A:  36.63  (  17.71   27.18   64.98 )

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      9     10     12     13     16     18     19     19     21     21     22     24     25     26     26     28     30     33     33 
GDT PERCENT_AT  17.14  25.71  28.57  34.29  37.14  45.71  51.43  54.29  54.29  60.00  60.00  62.86  68.57  71.43  74.29  74.29  80.00  85.71  94.29  94.29
GDT RMS_LOCAL    0.25   0.80   0.83   1.32   1.46   2.18   2.36   2.54   2.53   2.97   2.97   3.37   3.90   4.11   4.48   4.48   5.17   5.67   6.24   6.24
GDT RMS_ALL_AT   7.55   7.81   7.78   7.75   7.77   9.38   9.12   8.72   9.14   8.57   8.57   8.46   8.00   7.87   7.65   7.65   7.22   6.97   6.82   6.82

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  F     6_A      F     6_A
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A     9.009     0    0.198   0.673    11.545    0.833    0.635
LGA    D     2_A      D     2_A    10.149     0    0.609   1.076    12.326    0.476    0.238
LGA    E     3_A      E     3_A    12.506     0    0.554   0.868    15.915    0.000    0.000
LGA    M     4_A      M     4_A    12.857     0    0.582   0.874    16.858    0.000    0.000
LGA    W     5_A      W     5_A    13.999     0    0.083   1.191    20.195    0.000    0.000
LGA    F     6_A      F     6_A    13.521     0    0.541   0.706    14.314    0.000    0.000
LGA    C     7_A      C     7_A    15.325     0    0.575   0.517    18.012    0.000    0.000
LGA    E     8_A      E     8_A    16.531     0    0.016   0.876    19.591    0.000    0.000
LGA    T     9_A      T     9_A    18.887     0    0.019   0.302    22.130    0.000    0.000
LGA    L    10_A      L    10_A    14.730     0    0.088   0.092    17.410    0.000    0.000
LGA    R    11_A      R    11_A    12.786     0    0.459   1.043    17.576    0.000    0.000
LGA    R    12_A      R    12_A    10.930     0    0.653   1.543    21.053    2.976    1.082
LGA    L    13_A      L    13_A     4.173     0    0.628   1.101     6.688   43.095   38.988
LGA    L    14_A      L    14_A     3.619     0    0.639   1.210     8.320   48.690   31.905
LGA    C    15_A      C    15_A     5.262     0    0.102   0.893     8.599   36.071   26.190
LGA    P    16_A      P    16_A     3.250     0    0.077   0.069     4.163   53.810   48.435
LGA    K    17_A      K    17_A     2.503     0    0.060   0.820     3.964   57.143   52.487
LGA    S    18_A      S    18_A     3.039     0    0.129   0.146     5.255   63.214   53.730
LGA    C    19_A      C    19_A     1.484     0    0.075   0.106     2.777   72.976   70.317
LGA    S    20_A      S    20_A     3.217     0    0.064   0.572     4.386   50.476   48.175
LGA    I    21_A      I    21_A     3.059     0    0.074   0.174     4.930   53.571   47.857
LGA    E    22_A      E    22_A     2.157     0    0.048   0.631     3.990   68.810   60.159
LGA    G    23_A      G    23_A     1.841     0    0.664   0.664     4.005   61.905   61.905
LGA    G    24_A      G    24_A     1.513     0    0.181   0.181     1.735   77.143   77.143
LGA    C    25_A      C    25_A     0.740     0    0.171   0.737     2.823   90.476   84.921
LGA    P    26_A      P    26_A     2.005     0    0.428   0.430     3.258   65.119   62.789
LGA    E    27_A      E    27_A     2.079     0    0.209   0.969     3.549   64.762   62.381
LGA    V    28_A      V    28_A     2.312     0    0.023   1.198     4.521   73.095   62.653
LGA    C    29_A      C    29_A     0.920     0    0.053   0.728     3.659   83.810   75.238
LGA    S    30_A      S    30_A     2.776     0    0.094   0.561     3.503   59.286   56.270
LGA    H    31_A      H    31_A     3.000     0    0.320   1.219     7.795   50.357   33.571
LGA    M    32_A      M    32_A     1.348     0    0.067   1.131     4.861   63.571   63.095
LGA    C    33_A      C    33_A     6.537     0    0.583   0.557     9.048   13.333   12.302
LGA    P    34_A      P    34_A     9.604     0    0.507   0.540    10.607    1.905    2.789
LGA    L    35_A      L    35_A    11.137     0    0.325   1.445    13.768    0.000    0.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     6.756          6.577                  8.038           35.912   32.446

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     19    2.54    47.143    43.362     0.720

LGA_LOCAL      RMSD:   2.538  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.715  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   6.756  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.094008 * X  +   0.787050 * Y  +   0.609685 * Z  +   5.347493
  Y_new =   0.227923 * X  +   0.613146 * Y  +  -0.756375 * Z  +   8.106372
  Z_new =  -0.969130 * X  +   0.067856 * Y  +  -0.237027 * Z  +   4.094842 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.961995  1.321679  2.862772   [DEG:  112.4140   75.7266  164.0248 ]
ZXZ:  0.678426  1.810101 -1.500893   [DEG:   38.8710  103.7112  -85.9949 ]
 
# END of job
