
#######################################################
#                                                     #
#                        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   53 (  404),  selected   53 , name one
# Molecule2: number of CA atoms  105 (  764),  selected   53 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    53      29_B - 81_B        2.81     2.81
  LCS_AVERAGE:     50.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39      33_B - 71_B        1.98     3.22
  LCS_AVERAGE:     32.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      30_B - 51_B        0.99     4.23
  LCS_AVERAGE:     14.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   53
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     Y    29_B     Y    29_B     20   26   53      3    8   14   23   35   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    30_B     K    30_B     22   26   53     12   23   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    31_B     K    31_B     22   26   53      5   11   28   30   34   39   42   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     T    32_B     T    32_B     22   26   53      5   12   28   30   36   39   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     F    33_B     F    33_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     T    34_B     T    34_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    35_B     K    35_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    36_B     V    36_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     D    37_B     D    37_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    38_B     A    38_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    39_B     A    39_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     T    40_B     T    40_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    41_B     K    41_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    42_B     A    42_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     P    43_B     P    43_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     L    44_B     L    44_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    45_B     A    45_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     G    46_B     G    46_B     22   39   53      7   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    47_B     A    47_B     22   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    48_B     V    48_B     22   39   53     16   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     F    49_B     F    49_B     22   39   53     14   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     Q    50_B     Q    50_B     22   39   53      6   15   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    51_B     V    51_B     22   39   53      6   22   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    52_B     V    52_B     20   39   53      5   16   26   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     E    53_B     E    53_B     11   39   53      4   15   24   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    54_B     K    54_B      9   39   53      3    9   16   23   31   38   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     D    55_B     D    55_B      9   39   53      5    9   16   23   31   38   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     G    56_B     G    56_B      9   39   53      3    4   15   23   31   37   43   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     D    57_B     D    57_B      9   39   53      3    9   14   23   30   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     I    58_B     I    58_B     13   39   53      5   15   23   32   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     T    59_B     T    59_B     13   39   53      6   16   26   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     L    60_B     L    60_B     13   39   53      6   16   26   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     Y    61_B     Y    61_B     13   39   53      5   16   26   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     E    62_B     E    62_B     13   39   53      8   23   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     L    63_B     L    63_B     13   39   53     12   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     S    64_B     S    64_B     13   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     S    65_B     S    65_B     13   39   53     17   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     P    66_B     P    66_B     13   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     A    67_B     A    67_B     13   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     G    68_B     G    68_B     13   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     Y    69_B     Y    69_B     13   39   53     19   25   28   33   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    70_B     V    70_B     13   39   53     19   25   28   33   36   40   45   49   51   51   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     P    71_B     P    71_B      9   39   53      4    5   10   32   36   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     V    72_B     V    72_B      6   32   53      4    8   14   23   33   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     T    73_B     T    73_B      6   31   53      3    6    9   17   29   37   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     N    74_B     N    74_B      6   30   53      4    5    6   11   13   20   28   41   47   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     K    75_B     K    75_B      5   30   53      4    4    7   16   32   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     P    76_B     P    76_B      5   30   53      4    6   14   23   30   40   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     I    77_B     I    77_B      5    8   53      4    5    7   14   16   25   30   44   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     Y    78_B     Y    78_B      5    8   53      4    5    7   15   21   31   45   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     N    79_B     N    79_B      5    7   53      4    5    7   14   21   29   39   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     I    80_B     I    80_B      5    7   53      4    5    7   14   19   30   44   49   51   52   53   53   53   53   53   53   53   53   53   53 
LCS_GDT     S    81_B     S    81_B      5    7   53      0    5    6    8   12   18   19   37   43   52   53   53   53   53   53   53   53   53   53   53 
LCS_AVERAGE  LCS_A:  32.50  (  14.41   32.61   50.48 )

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     19     25     28     33     36     40     45     49     51     52     53     53     53     53     53     53     53     53     53     53 
GDT PERCENT_AT  18.10  23.81  26.67  31.43  34.29  38.10  42.86  46.67  48.57  49.52  50.48  50.48  50.48  50.48  50.48  50.48  50.48  50.48  50.48  50.48
GDT RMS_LOCAL    0.32   0.53   0.72   1.13   1.36   1.89   2.26   2.50   2.60   2.80   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81
GDT RMS_ALL_AT   4.55   4.37   4.27   3.78   3.56   3.13   2.91   2.83   2.83   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81

# Checking swapping
#   possible swapping detected:  Y    29_B      Y    29_B
#   possible swapping detected:  F    33_B      F    33_B
#   possible swapping detected:  E    53_B      E    53_B
#   possible swapping detected:  D    57_B      D    57_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y    29_B      Y    29_B     2.867     0    0.610   0.806     6.548   47.619   40.238
LGA    K    30_B      K    30_B     2.684     0    0.094   0.284     3.228   55.476   59.841
LGA    K    31_B      K    31_B     4.237     0    0.093   1.000     5.912   43.452   32.804
LGA    T    32_B      T    32_B     3.403     0    0.128   0.169     3.966   46.667   46.190
LGA    F    33_B      F    33_B     2.067     0    0.047   1.258     7.822   68.810   45.541
LGA    T    34_B      T    34_B     1.922     0    0.093   0.117     2.589   68.929   67.143
LGA    K    35_B      K    35_B     1.225     0    0.049   0.196     2.214   81.429   81.587
LGA    V    36_B      V    36_B     1.744     0    0.027   0.031     2.353   72.857   69.388
LGA    D    37_B      D    37_B     1.636     0    0.035   0.078     2.219   68.810   74.048
LGA    A    38_B      A    38_B     2.590     0    0.043   0.048     3.278   57.262   57.238
LGA    A    39_B      A    39_B     2.675     0    0.046   0.055     3.211   57.262   58.762
LGA    T    40_B      T    40_B     2.811     0    0.025   0.092     3.235   55.357   58.299
LGA    K    41_B      K    41_B     2.859     0    0.102   1.048     7.669   55.357   43.016
LGA    A    42_B      A    42_B     2.223     0    0.025   0.035     2.250   68.810   68.000
LGA    P    43_B      P    43_B     1.830     0    0.020   0.330     2.174   72.976   71.837
LGA    L    44_B      L    44_B     0.784     0    0.080   0.126     1.136   88.214   89.345
LGA    A    45_B      A    45_B     1.448     0    0.025   0.037     1.709   79.286   78.000
LGA    G    46_B      G    46_B     2.117     0    0.127   0.127     2.117   68.810   68.810
LGA    A    47_B      A    47_B     1.148     0    0.068   0.083     1.231   83.690   85.048
LGA    V    48_B      V    48_B     1.131     0    0.021   0.038     1.848   79.286   77.755
LGA    F    49_B      F    49_B     1.312     0    0.065   0.087     2.043   83.690   79.177
LGA    Q    50_B      Q    50_B     1.970     0    0.024   0.268     3.209   75.000   65.132
LGA    V    51_B      V    51_B     1.496     0    0.034   1.200     4.193   79.286   71.429
LGA    V    52_B      V    52_B     1.414     0    0.040   1.105     2.906   81.429   74.354
LGA    E    53_B      E    53_B     1.067     0    0.161   0.789     3.706   67.738   71.640
LGA    K    54_B      K    54_B     3.641     0    0.171   0.625     9.881   52.024   30.000
LGA    D    55_B      D    55_B     3.973     0    0.350   0.827     6.821   37.262   31.667
LGA    G    56_B      G    56_B     4.330     0    0.106   0.106     4.330   38.690   38.690
LGA    D    57_B      D    57_B     3.295     0    0.403   1.064     4.771   57.381   53.214
LGA    I    58_B      I    58_B     2.149     0    0.198   1.270     6.054   62.857   55.952
LGA    T    59_B      T    59_B     2.199     0    0.044   1.074     4.485   64.762   61.973
LGA    L    60_B      L    60_B     2.180     0    0.081   0.134     2.253   64.762   67.798
LGA    Y    61_B      Y    61_B     2.192     0    0.071   1.311     9.369   62.857   38.452
LGA    E    62_B      E    62_B     2.184     0    0.104   0.575     4.532   64.762   57.725
LGA    L    63_B      L    63_B     2.149     0    0.054   1.045     3.507   62.857   64.167
LGA    S    64_B      S    64_B     2.454     0    0.084   0.104     2.634   64.762   63.492
LGA    S    65_B      S    65_B     2.193     0    0.035   0.571     2.726   66.786   64.841
LGA    P    66_B      P    66_B     1.535     0    0.044   0.054     1.767   72.857   76.531
LGA    A    67_B      A    67_B     1.921     0    0.022   0.024     2.005   72.857   71.238
LGA    G    68_B      G    68_B     1.739     0    0.030   0.030     1.853   75.000   75.000
LGA    Y    69_B      Y    69_B     1.729     0    0.090   0.160     2.384   68.810   77.262
LGA    V    70_B      V    70_B     2.602     0    0.091   1.151     4.560   69.048   59.252
LGA    P    71_B      P    71_B     1.956     0    0.086   0.104     3.527   77.381   65.714
LGA    V    72_B      V    72_B     2.516     0    0.070   0.236     3.549   57.262   56.327
LGA    T    73_B      T    73_B     3.938     0    0.538   0.451     5.033   45.119   39.320
LGA    N    74_B      N    74_B     6.402     0    0.400   0.392    12.929   26.786   13.750
LGA    K    75_B      K    75_B     2.890     0    0.061   0.968    10.758   48.690   28.730
LGA    P    76_B      P    76_B     3.147     0    0.054   0.321     5.823   48.929   40.068
LGA    I    77_B      I    77_B     4.665     0    0.543   1.658    10.214   43.690   24.286
LGA    Y    78_B      Y    78_B     3.511     0    0.008   0.272     4.754   43.333   44.087
LGA    N    79_B      N    79_B     4.205     0    0.116   0.939     4.615   41.786   44.583
LGA    I    80_B      I    80_B     3.913     0    0.632   0.909     4.149   40.238   41.845
LGA    S    81_B      S    81_B     6.081     0    0.540   0.895     7.619   15.476   13.730

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       53     212    212  100.00     404    404  100.00               105
SUMMARY(RMSD_GDC):     2.809          2.779                  3.555           30.995   28.898

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53  105    4.0     49    2.50    38.095    38.200     1.882

LGA_LOCAL      RMSD:   2.504  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.831  Number of assigned atoms:   53 
Std_ASGN_ATOMS RMSD:   2.809  Standard rmsd on all 53 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.550202 * X  +   0.833856 * Y  +  -0.044299 * Z  + -41.096161
  Y_new =   0.022341 * X  +   0.067731 * Y  +   0.997453 * Z  + -76.879318
  Z_new =   0.834733 * X  +   0.547811 * Y  +  -0.055895 * Z  + -97.834694 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.101009 -0.987648  1.672478   [DEG:  177.6747  -56.5880   95.8260 ]
ZXZ: -3.097210  1.626721  0.990026   [DEG: -177.4571   93.2042   56.7243 ]
 
# END of job
