
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.69     6.78
  LCS_AVERAGE:     83.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.72    11.17
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.65    11.60
  LCS_AVERAGE:     37.87

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     8_D     L     8_F      3    3   19      0    3    3    3    3    3    4    7   14   15   16   17   17   19   22   22   22   25   25   25 
LCS_GDT     Q     9_D     Q     9_F      3    4   19      3    3    3    5    6    9   11   13   14   15   16   18   20   21   24   24   24   25   25   25 
LCS_GDT     K    10_D     K    10_F      3    4   19      3    4    5    5    6    6    7    8   10   12   14   17   20   21   24   24   24   25   25   25 
LCS_GDT     L    11_D     L    11_F      3   12   21      3    4    5    5    7   11   12   13   14   15   16   18   20   21   24   24   24   25   25   25 
LCS_GDT     N    12_D     N    12_F     10   12   22      8    8    9   11   11   11   12   13   14   16   17   20   20   21   24   24   24   25   25   25 
LCS_GDT     S    13_D     S    13_F     10   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     W    14_D     W    14_F     10   12   22      8    8    9   11   11   11   12   13   14   15   16   17   18   20   24   24   24   25   25   25 
LCS_GDT     D    15_D     D    15_F     10   12   22      8    8    9   11   11   11   12   13   14   16   17   20   20   21   24   24   24   25   25   25 
LCS_GDT     V    16_D     V    16_F     10   12   22      8    8    9   11   11   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     F    17_D     F    17_F     10   12   22      8    8    9   11   11   11   12   13   14   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     G    18_D     G    18_F     10   12   22      8    8    9   11   11   11   12   14   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     N    19_D     N    19_F     10   12   22      8    8    9   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     W    20_D     W    20_F     10   12   22      3    5    9   11   11   11   12   14   15   15   16   18   18   19   21   22   22   24   24   25 
LCS_GDT     F    21_D     F    21_F     10   13   22      3    4    9   11   11   11   13   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      8   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     R    32_D     R    32_F     12   13   22      8   11   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    4   11   13   13   14   14   15   16   16   18   20   20   21   24   24   24   25   25   25 
LCS_AVERAGE  LCS_A:  55.13  (  37.87   44.38   83.14 )

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      9     11     11     13     13     14     14     15     16     16     18     20     20     21     24     24     24     25     25     25 
GDT PERCENT_AT  34.62  42.31  42.31  50.00  50.00  53.85  53.85  57.69  61.54  61.54  69.23  76.92  76.92  80.77  92.31  92.31  92.31  96.15  96.15  96.15
GDT RMS_LOCAL    0.24   0.39   0.39   0.97   0.97   1.73   1.73   2.15   2.61   2.61   3.52   4.10   4.10   4.52   5.12   5.12   5.12   5.47   5.47   5.47
GDT RMS_ALL_AT  11.42  11.64  11.64  10.75  10.75   9.35   9.35   9.55   8.85   8.85   7.89   6.77   6.77   6.19   5.85   5.85   5.85   5.79   5.79   5.79

# Checking swapping
#   possible swapping detected:  D    15_D      D    15_F
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  F    21_D      F    21_F
#   possible swapping detected:  D    22_D      D    22_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    24.046     0    0.293   0.290    26.840    0.000    0.000
LGA    Q     9_D      Q     9_F    17.603     0    0.597   0.626    20.100    0.000    0.000
LGA    K    10_D      K    10_F    18.479     0    0.058   0.548    23.268    0.000    0.000
LGA    L    11_D      L    11_F    16.239     0    0.602   0.672    17.738    0.000    0.000
LGA    N    12_D      N    12_F    13.016     0    0.616   0.875    16.936    0.357    0.179
LGA    S    13_D      S    13_F    12.118     0    0.043   0.069    14.358    0.000    0.000
LGA    W    14_D      W    14_F    14.606     0    0.032   1.188    23.020    0.000    0.000
LGA    D    15_D      D    15_F    10.171     0    0.056   0.884    13.856    6.786    3.393
LGA    V    16_D      V    16_F     4.116     0    0.040   0.050     6.211   29.405   34.762
LGA    F    17_D      F    17_F     9.322     0    0.031   1.295    18.076    4.524    1.645
LGA    G    18_D      G    18_F     6.871     0    0.226   0.226     7.630   26.905   26.905
LGA    N    19_D      N    19_F     1.833     0    0.259   0.659     7.144   54.643   40.060
LGA    W    20_D      W    20_F     6.337     0    0.086   1.164    16.262   20.595    6.293
LGA    F    21_D      F    21_F     4.692     0    0.584   1.040    10.855   44.405   20.130
LGA    D    22_D      D    22_F     2.500     0    0.572   1.244     6.999   64.881   41.845
LGA    L    23_D      L    23_F     2.238     0    0.094   1.014     5.084   66.786   59.107
LGA    A    24_D      A    24_F     1.967     0    0.018   0.019     2.283   72.976   71.333
LGA    S    25_D      S    25_F     1.524     0    0.150   0.728     2.110   79.405   77.302
LGA    W    26_D      W    26_F     1.216     0    0.039   0.335     2.700   85.952   75.612
LGA    I    27_D      I    27_F     0.572     0    0.045   0.123     1.337   95.238   91.786
LGA    K    28_D      K    28_F     0.566     0    0.107   0.237     1.588   95.238   88.624
LGA    Y    29_D      Y    29_F     0.316     0    0.034   0.357     1.434   97.619   91.389
LGA    I    30_D      I    30_F     0.890     0    0.058   0.623     2.530   88.333   79.702
LGA    Q    31_D      Q    31_F     1.593     0    0.034   1.279     6.512   72.976   53.175
LGA    R    32_D      R    32_F     1.255     0    0.424   0.847     4.854   79.286   66.580
LGA    R    33_D      R    33_F     1.619     0    0.607   0.558     8.335   72.976   44.805

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.775          5.607                  7.586           44.588   37.486

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.15    60.577    55.511     0.666

LGA_LOCAL      RMSD:   2.153  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.548  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.775  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.828604 * X  +  -0.532610 * Y  +   0.172459 * Z  +  41.945522
  Y_new =  -0.539135 * X  +   0.842154 * Y  +   0.010494 * Z  + -64.546478
  Z_new =  -0.150826 * X  +  -0.084283 * Y  +  -0.984961 * Z  +  -4.778964 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.564757  0.151404 -3.056231   [DEG: -146.9498    8.6748 -175.1091 ]
ZXZ:  1.631573  2.967944 -2.080376   [DEG:   93.4823  170.0506 -119.1968 ]
 
# END of job
