
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , 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:    50       6_C - 55_C        4.68     5.05
  LCS_AVERAGE:     96.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    44       6_C - 49_C        1.96     5.88
  LCS_AVERAGE:     75.93

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      28_C - 47_C        0.88     6.05
  LCS_AVERAGE:     29.60

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3   44   50      3    3    3    4    7    8   10   29   42   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     T     7_C     T     7_C     18   44   50      7   18   29   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     K     8_C     K     8_C     18   44   50      8   26   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     I     9_C     I     9_C     18   44   50     10   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     L    10_C     L    10_C     18   44   50     15   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     P    11_C     P    11_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     C    12_C     C    12_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     P    13_C     P    13_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     R    14_C     R    14_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     C    15_C     C    15_C     18   44   50      7   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     N    16_C     N    16_C     18   44   50      3    7   33   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     S    17_C     S    17_C     18   44   50      6   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     M    18_C     M    18_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     E    19_C     E    19_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     T    20_C     T    20_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     K    21_C     K    21_C     18   44   50     11   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     F    22_C     F    22_C     18   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     C    23_C     C    23_C     18   44   50     16   27   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Y    24_C     Y    24_C     18   44   50      4   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Y    25_C     Y    25_C      3   44   50      3    3    4    6    7    7   37   40   43   43   43   44   46   47   47   48   49   49   49   50 
LCS_GDT     N    26_C     N    26_C      3   44   50      3    7   21   35   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     N    27_C     N    27_C      3   44   50      3    3    4    6    7   33   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Y    28_C     Y    28_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     N    29_C     N    29_C     20   44   50      3   25   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     V    30_C     V    30_C     20   44   50     11   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     N    31_C     N    31_C     20   44   50     11   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Q    32_C     Q    32_C     20   44   50     11   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     P    33_C     P    33_C     20   44   50      8   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     R    34_C     R    34_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     H    35_C     H    35_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     F    36_C     F    36_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     C    37_C     C    37_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     K    38_C     K    38_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     A    39_C     A    39_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     C    40_C     C    40_C     20   44   50     16   27   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Q    41_C     Q    41_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     R    42_C     R    42_C     20   44   50     16   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     Y    43_C     Y    43_C     20   44   50     13   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     W    44_C     W    44_C     20   44   50      8   27   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     T    45_C     T    45_C     20   44   50      3    4   33   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     S    46_C     S    46_C     20   44   50      8   27   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     G    47_C     G    47_C     20   44   50      9   28   35   37   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     G    48_C     G    48_C      4   44   50      3    3   13   31   39   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     T    49_C     T    49_C      4   44   50      3    6   13   25   37   40   41   42   43   43   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     M    50_C     M    50_C      4    6   50      2    4    5    5    6    7   12   18   25   32   43   45   46   47   47   48   49   49   49   50 
LCS_GDT     R    51_C     R    51_C      4    6   50      3    4    5    5    5    7   11   15   22   30   36   45   46   47   47   48   49   49   49   50 
LCS_GDT     S    52_C     S    52_C      4    6   50      3    4    5    5    5    7   11   15   16   18   21   26   33   36   42   47   49   49   49   50 
LCS_GDT     V    53_C     V    53_C      4    6   50      3    4    5    5    7    7   11   16   25   31   37   45   46   47   47   48   49   49   49   50 
LCS_GDT     P    54_C     P    54_C      4    6   50      3    4    5    5    5    7   11   15   16   20   27   30   35   39   46   48   49   49   49   50 
LCS_GDT     I    55_C     I    55_C      3    6   50      3    3    3    5    5    7    7   11   16   18   19   20   23   27   29   31   32   40   42   46 
LCS_GDT     G    56_C     G    56_C      3    3   16      3    3    3    3    6    7   11   15   16   18   19   21   31   34   38   39   44   49   49   50 
LCS_AVERAGE  LCS_A:  67.42  (  29.60   75.93   96.73 )

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     16     28     35     37     39     40     41     42     43     43     43     45     46     47     47     48     49     49     49     50 
GDT PERCENT_AT  31.37  54.90  68.63  72.55  76.47  78.43  80.39  82.35  84.31  84.31  84.31  88.24  90.20  92.16  92.16  94.12  96.08  96.08  96.08  98.04
GDT RMS_LOCAL    0.29   0.66   0.83   0.90   1.10   1.22   1.33   1.49   1.71   1.71   1.71   2.66   2.78   3.14   3.14   3.68   4.04   4.04   4.04   4.52
GDT RMS_ALL_AT   6.26   6.01   5.99   6.02   6.03   5.92   5.93   5.89   5.92   5.92   5.92   5.53   5.56   5.41   5.41   5.23   5.14   5.14   5.14   5.06

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    25_C      Y    25_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     6.562     2    0.669   0.601     7.469   15.714   10.408
LGA    T     7_C      T     7_C     2.376     0    0.622   0.990     4.200   59.167   57.687
LGA    K     8_C      K     8_C     1.489     4    0.021   0.030     1.717   79.286   43.333
LGA    I     9_C      I     9_C     0.669     0    0.036   0.144     1.246   90.476   91.726
LGA    L    10_C      L    10_C     0.327     0    0.025   0.101     0.971  100.000   97.619
LGA    P    11_C      P    11_C     0.265     0    0.010   0.031     0.432  100.000  100.000
LGA    C    12_C      C    12_C     0.218     0    0.046   0.076     0.561   97.619   98.413
LGA    P    13_C      P    13_C     0.663     0    0.019   0.254     1.457   90.476   89.184
LGA    R    14_C      R    14_C     0.765     0    0.200   0.308     2.100   86.071   83.333
LGA    C    15_C      C    15_C     0.974     0    0.589   0.920     2.845   79.881   77.619
LGA    N    16_C      N    16_C     1.796     0    0.395   0.657     4.111   68.929   59.881
LGA    S    17_C      S    17_C     0.907     0    0.062   0.137     1.186   90.595   90.556
LGA    M    18_C      M    18_C     0.653     0    0.018   0.469     1.124   90.476   89.405
LGA    E    19_C      E    19_C     0.508     4    0.062   0.060     0.777   92.857   51.323
LGA    T    20_C      T    20_C     0.589     0    0.037   0.110     0.992   90.476   94.558
LGA    K    21_C      K    21_C     1.202     0    0.031   0.429     1.998   88.214   80.635
LGA    F    22_C      F    22_C     0.453     0    0.066   1.360     7.881   90.595   57.403
LGA    C    23_C      C    23_C     1.277     0    0.574   0.604     3.841   72.024   75.159
LGA    Y    24_C      Y    24_C     0.741     0    0.699   1.330    11.781   68.810   33.413
LGA    Y    25_C      Y    25_C     5.892     0    0.608   1.445    16.905   33.333   11.508
LGA    N    26_C      N    26_C     3.335     0    0.620   0.761     5.204   50.357   44.702
LGA    N    27_C      N    27_C     4.394     0    0.163   0.834     9.299   42.143   24.107
LGA    Y    28_C      Y    28_C     0.886     0    0.242   1.205    10.768   83.810   43.730
LGA    N    29_C      N    29_C     1.310     0    0.055   0.200     2.192   81.548   74.167
LGA    V    30_C      V    30_C     1.084     0    0.411   0.425     2.717   75.357   73.129
LGA    N    31_C      N    31_C     0.952     0    0.117   0.622     3.832   90.476   77.024
LGA    Q    32_C      Q    32_C     0.795     0    0.050   0.324     1.657   88.214   84.497
LGA    P    33_C      P    33_C     1.219     0    0.180   0.198     1.712   81.548   81.497
LGA    R    34_C      R    34_C     0.607     0    0.171   1.261     5.611   90.476   68.961
LGA    H    35_C      H    35_C     0.923     0    0.075   0.204     1.719   90.476   83.333
LGA    F    36_C      F    36_C     0.693     0    0.033   0.079     1.040   90.476   89.654
LGA    C    37_C      C    37_C     0.506     0    0.049   0.135     0.620   92.857   93.651
LGA    K    38_C      K    38_C     0.402     0    0.091   0.447     1.689   95.238   93.810
LGA    A    39_C      A    39_C     0.780     0    0.159   0.175     0.901   90.476   90.476
LGA    C    40_C      C    40_C     1.054     0    0.017   0.754     3.274   85.952   79.206
LGA    Q    41_C      Q    41_C     0.661     0    0.075   0.091     1.135   90.476   86.455
LGA    R    42_C      R    42_C     0.605     0    0.041   1.492     6.483   90.476   65.195
LGA    Y    43_C      Y    43_C     1.123     0    0.048   0.070     1.602   83.690   80.754
LGA    W    44_C      W    44_C     1.249     0    0.064   0.152     1.318   81.429   86.599
LGA    T    45_C      T    45_C     1.751     0    0.146   1.178     3.836   70.833   65.238
LGA    S    46_C      S    46_C     1.129     0    0.629   0.799     2.985   75.357   77.460
LGA    G    47_C      G    47_C     1.196     0    0.694   0.694     2.166   81.905   81.905
LGA    G    48_C      G    48_C     3.110     0    0.102   0.102     3.110   55.476   55.476
LGA    T    49_C      T    49_C     3.650     0    0.674   1.005     6.100   32.976   36.531
LGA    M    50_C      M    50_C    10.017     0    0.672   1.028    12.441    1.786    0.893
LGA    R    51_C      R    51_C    10.620     0    0.213   0.885    11.727    0.119    5.065
LGA    S    52_C      S    52_C    15.195     0    0.263   0.677    19.400    0.000    0.000
LGA    V    53_C      V    53_C    11.791     0    0.613   1.508    14.270    0.000    2.313
LGA    P    54_C      P    54_C    16.104     0    0.621   0.511    17.431    0.000    0.000
LGA    I    55_C      I    55_C    20.588     0    0.610   0.448    26.183    0.000    0.000
LGA    G    56_C      G    56_C    18.184     0    0.692   0.692    18.531    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     5.028          5.005                  5.613           68.214   61.549

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     42    1.49    75.980    77.875     2.648

LGA_LOCAL      RMSD:   1.486  Number of atoms:   42  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.887  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   5.028  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.593390 * X  +   0.768177 * Y  +  -0.240401 * Z  + -22.027435
  Y_new =   0.042281 * X  +   0.328002 * Y  +   0.943730 * Z  + -33.219063
  Z_new =   0.803804 * X  +   0.549836 * Y  +  -0.227113 * Z  +  -4.097346 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.070459 -0.933662  1.962506   [DEG:  175.9243  -53.4949  112.4433 ]
ZXZ: -2.892162  1.799908  0.970860   [DEG: -165.7087  103.1271   55.6262 ]
 
# END of job
