
#######################################################
#                                                     #
#                        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   33 (  253),  selected   33 , name one
# Molecule2: number of CA atoms   79 (  632),  selected   33 , 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:    33       4_A - 36_A        2.67     2.67
  LCS_AVERAGE:     41.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       4_A - 19_A        1.82     2.77
  LCS_AVERAGE:     16.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       5_A - 12_A        0.98     3.44
  LONGEST_CONTINUOUS_SEGMENT:     8       6_A - 13_A        0.97     4.24
  LONGEST_CONTINUOUS_SEGMENT:     8      27_A - 34_A        0.87     3.41
  LCS_AVERAGE:      8.55

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     L     4_A     L     4_A      7   16   33      5    6   13   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L     5_A     L     5_A      8   16   33      5    6   16   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     C     6_A     C     6_A      8   16   33      6   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     P     7_A     P     7_A      8   16   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     N     8_A     N     8_A      8   16   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     C     9_A     C     9_A      8   16   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     Q    10_A     Q    10_A      8   16   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    11_A     V    11_A      8   16   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    12_A     G    12_A      8   16   33      4   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     M    13_A     M    13_A      8   16   33      3    5    9   13   23   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R    14_A     R    14_A      6   16   33      3   12   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     E    15_A     E    15_A      6   16   33      3    5    9   19   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    16_A     V    16_A      6   16   33      3   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     E    17_A     E    17_A      6   16   33      3    5    9   19   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R    18_A     R    18_A      6   16   33      3   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R    19_A     R    19_A      6   16   33      3    5    9   19   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    20_A     G    20_A      3   10   33      3    4    6    8   10   16   20   28   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    21_A     V    21_A      5    7   33      3    5   13   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L    22_A     L    22_A      5    7   33      4    4    6   11   20   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     I    23_A     I    23_A      5   12   33      4    9   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     D    24_A     D    24_A      5   12   33      4    5   11   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    25_A     V    25_A      6   12   33      4    5    7    8   11   16   21   26   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     C    26_A     C    26_A      7   12   33      4    6   12   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     P    27_A     P    27_A      8   12   33      4    6   12   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     Q    28_A     Q    28_A      8   12   33      6   10   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     C    29_A     C    29_A      8   12   33      6   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    30_A     G    30_A      8   12   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G    31_A     G    31_A      8   12   33      7   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V    32_A     V    32_A      8   12   33      6   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     W    33_A     W    33_A      8   12   33      6   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L    34_A     L    34_A      8   12   33      5   14   17   21   25   27   29   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     D    35_A     D    35_A      4   10   33      3    4    4    4    6   18   26   30   31   32   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     K    36_A     K    36_A      4    6   33      3    4    4    8   10   11   25   28   30   32   33   33   33   33   33   33   33   33   33   33 
LCS_AVERAGE  LCS_A:  22.40  (   8.55   16.88   41.77 )

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      7     14     17     21     25     27     29     30     31     32     33     33     33     33     33     33     33     33     33     33 
GDT PERCENT_AT   8.86  17.72  21.52  26.58  31.65  34.18  36.71  37.97  39.24  40.51  41.77  41.77  41.77  41.77  41.77  41.77  41.77  41.77  41.77  41.77
GDT RMS_LOCAL    0.33   0.70   0.80   1.13   1.52   1.71   1.91   2.09   2.26   2.47   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67
GDT RMS_ALL_AT   3.79   3.46   3.47   3.39   3.01   2.83   2.79   2.72   2.73   2.70   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67

# Checking swapping
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  D    24_A      D    24_A
#   possible swapping detected:  D    35_A      D    35_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     4_A      L     4_A     1.853     0    0.089   0.122     2.880   68.929   72.024
LGA    L     5_A      L     5_A     1.228     4    0.077   0.077     1.359   85.952   42.976
LGA    C     6_A      C     6_A     0.651     0    0.000   0.080     0.878   92.857   92.063
LGA    P     7_A      P     7_A     0.518     0    0.165   0.239     0.969   97.619   94.558
LGA    N     8_A      N     8_A     0.261     0    0.145   0.904     1.998   90.833   85.119
LGA    C     9_A      C     9_A     1.314     0    0.125   0.200     1.721   81.548   80.079
LGA    Q    10_A      Q    10_A     1.785     0    0.067   1.046     3.422   72.976   63.439
LGA    V    11_A      V    11_A     1.558     0    0.098   1.140     3.063   77.143   71.020
LGA    G    12_A      G    12_A     1.502     0    0.055   0.055     2.900   69.048   69.048
LGA    M    13_A      M    13_A     3.372     0    0.112   0.696    10.905   57.500   32.321
LGA    R    14_A      R    14_A     1.130     0    0.031   1.065    13.062   71.429   31.558
LGA    E    15_A      E    15_A     2.228     0    0.081   0.598    10.797   67.262   34.444
LGA    V    16_A      V    16_A     1.940     0    0.000   0.057     6.207   77.738   54.422
LGA    E    17_A      E    17_A     2.570     0    0.094   0.882    11.660   57.976   28.942
LGA    R    18_A      R    18_A     2.835     3    0.621   0.725    10.175   71.071   29.870
LGA    R    19_A      R    19_A     2.408     5    0.260   0.411     5.060   54.524   26.147
LGA    G    20_A      G    20_A     6.352     0    0.047   0.047     6.540   22.024   22.024
LGA    V    21_A      V    21_A     1.312     0    0.376   1.028     4.175   60.119   64.762
LGA    L    22_A      L    22_A     3.624     0    0.166   0.920    11.044   57.619   31.905
LGA    I    23_A      I    23_A     1.695     0    0.049   1.172     9.087   67.619   43.571
LGA    D    24_A      D    24_A     1.744     0    0.000   0.821     7.097   65.595   45.119
LGA    V    25_A      V    25_A     5.371     0    0.578   0.919     9.564   30.595   18.639
LGA    C    26_A      C    26_A     2.152     0    0.150   0.775     2.962   62.857   62.222
LGA    P    27_A      P    27_A     2.676     0    0.068   0.377     3.473   57.262   57.279
LGA    Q    28_A      Q    28_A     2.178     0    0.242   0.891     6.751   70.833   53.333
LGA    C    29_A      C    29_A     1.765     0    0.071   0.739     1.881   72.857   72.857
LGA    G    30_A      G    30_A     1.802     0    0.000   0.000     1.841   72.857   72.857
LGA    G    31_A      G    31_A     1.424     0    0.077   0.077     1.728   75.000   75.000
LGA    V    32_A      V    32_A     1.484     0    0.077   1.109     4.345   81.429   75.170
LGA    W    33_A      W    33_A     1.076     0    0.576   0.831     3.455   71.429   67.483
LGA    L    34_A      L    34_A     1.584     0    0.076   0.744     8.626   61.905   38.988
LGA    D    35_A      D    35_A     4.680     0    0.000   1.102     9.132   49.524   27.560
LGA    K    36_A      K    36_A     6.674     0    0.130   1.342     7.548   17.262   14.497

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     241    241  100.00                79
SUMMARY(RMSD_GDC):     2.672          2.630                  4.556           27.737   22.168

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   79    4.0     30    2.09    31.013    29.275     1.372

LGA_LOCAL      RMSD:   2.086  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.721  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   2.672  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.075948 * X  +   0.329210 * Y  +   0.941197 * Z  + -368.789886
  Y_new =   0.898034 * X  +   0.387622 * Y  +  -0.208047 * Z  + -269.679443
  Z_new =  -0.433320 * X  +   0.861028 * Y  +  -0.266203 * Z  + -34.410927 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.486425  0.448174  1.870643   [DEG:   85.1659   25.6785  107.1800 ]
ZXZ:  1.353249  1.840248 -0.466251   [DEG:   77.5355  105.4384  -26.7142 ]
 
# END of job
