
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , 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:    29      30_A - 58_A        4.53    14.95
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.42    15.19
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.56    15.19
  LCS_AVERAGE:     29.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     A     1_A     A     1_A      3   14   17      3    3    3    4   12   22   27   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     29   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   28   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    6   30   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      3   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    5   10   14   16   22   33   37   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     10   14   14   14   15   15   18   28   31   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   23   31   34   40   41   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   26   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   24   25   28   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     12   14   14   14   15   15   16   19   21   22   22   22   22   23   25   27   31   34   36   41 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    4   14   14   15   15   16   19   21   22   22   22   26   29   37   41   42   43   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   15   19   21   22   22   26   28   32   44   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   14   16   19   21   22   22   22   25   40   44   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    9   12   21   30   36   40   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    3    5    5    6   11   22   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29     26   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   33   35   36   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    7   34   37   37   37   38   39   40   41   41   42   42   44   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.38  (  29.49   32.82   43.85 )

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     31     33     35     36     37     37     37     38     39     40     41     41     42     42     44     44     44     45     46     46 
GDT PERCENT_AT  53.45  56.90  60.34  62.07  63.79  63.79  63.79  65.52  67.24  68.97  70.69  70.69  72.41  72.41  75.86  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.23   0.28   0.46   0.60   0.73   0.73   0.73   1.34   1.64   1.96   2.26   2.26   2.69   2.69   3.63   3.63   3.63   3.98   4.40   4.40
GDT RMS_ALL_AT  15.21  15.20  15.20  15.21  15.19  15.19  15.19  15.15  15.10  15.02  14.92  14.92  14.89  14.89  14.75  14.75  14.75  14.63  14.52  14.52

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.341     0    0.517   0.566     7.839   26.190   22.381
LGA    E     2_A      E     2_A     0.759     0    0.652   1.136     7.541   84.048   48.466
LGA    Y     3_A      Y     3_A     0.392     0    0.010   0.146     0.594  100.000   99.206
LGA    V     4_A      V     4_A     0.280     0    0.036   0.044     0.391  100.000  100.000
LGA    R     5_A      R     5_A     0.113     0    0.023   0.177     1.476  100.000   94.069
LGA    A     6_A      A     6_A     0.393     0    0.057   0.060     0.530  100.000   98.095
LGA    L     7_A      L     7_A     0.363     0    0.053   0.079     0.656   97.619   98.810
LGA    F     8_A      F     8_A     0.443     0    0.029   0.126     0.803  100.000   97.403
LGA    D     9_A      D     9_A     0.485     0    0.046   0.190     1.444   95.238   91.726
LGA    H    10_A      H    10_A     0.534     0    0.026   1.144     2.518   92.857   85.571
LGA    T    11_A      T    11_A     1.128     0    0.656   0.948     3.444   75.833   74.762
LGA    G    12_A      G    12_A     1.120     0    0.074   0.074     1.199   85.952   85.952
LGA    H    13_A      H    13_A     2.312     0    0.649   1.238     5.323   56.548   51.333
LGA    D    14_A      D    14_A     2.061     0    0.114   1.220     5.466   52.381   52.143
LGA    E    15_A      E    15_A     7.335     0    0.714   1.200    13.246   15.357    7.460
LGA    Q    16_A      Q    16_A     8.129     0    0.655   1.227    10.157    4.048    3.651
LGA    E    17_A      E    17_A    12.231     0    0.040   0.995    15.835    0.000    0.000
LGA    L    18_A      L    18_A    19.232     0    0.107   1.364    23.365    0.000    0.000
LGA    P    19_A      P    19_A    24.902     0    0.050   0.340    27.651    0.000    0.000
LGA    F    20_A      F    20_A    30.714     0    0.037   1.450    32.895    0.000    0.000
LGA    K    21_A      K    21_A    37.608     0    0.027   0.094    40.189    0.000    0.000
LGA    K    22_A      K    22_A    40.442     0    0.028   0.534    48.814    0.000    0.000
LGA    G    23_A      G    23_A    42.322     0    0.021   0.021    42.322    0.000    0.000
LGA    E    24_A      E    24_A    38.665     0    0.018   1.010    39.545    0.000    0.000
LGA    I    25_A      I    25_A    36.266     0    0.086   0.637    41.076    0.000    0.000
LGA    L    26_A      L    26_A    29.817     0    0.031   0.088    31.886    0.000    0.000
LGA    R    27_A      R    27_A    28.128     0    0.086   1.335    32.739    0.000    0.000
LGA    I    28_A      I    28_A    20.985     0    0.011   0.071    23.725    0.000    0.000
LGA    R    29_A      R    29_A    20.782     0    0.599   1.210    30.727    0.000    0.000
LGA    D    30_A      D    30_A    16.750     0    0.687   0.852    21.261    0.000    0.000
LGA    K    31_A      K    31_A    14.556     0    0.270   0.265    21.391    0.000    0.000
LGA    P    32_A      P    32_A    13.633     0    0.070   0.370    15.970    0.000    0.000
LGA    E    33_A      E    33_A    10.685     0    0.691   1.056    13.974    1.071    0.476
LGA    E    34_A      E    34_A     6.582     0    0.217   1.121     9.337   21.667   12.222
LGA    Q    35_A      Q    35_A     0.538     0    0.650   0.679     5.449   86.429   66.085
LGA    L    36_A      L    36_A     0.791     0    0.157   0.598     1.658   90.595   86.071
LGA    W    37_A      W    37_A     0.503     0    0.070   0.260     1.700   95.238   88.707
LGA    N    38_A      N    38_A     0.481     0    0.053   0.555     1.923   97.619   88.512
LGA    A    39_A      A    39_A     0.257     0    0.024   0.033     0.344  100.000  100.000
LGA    E    40_A      E    40_A     0.165     0    0.049   0.509     1.539  100.000   95.926
LGA    N    41_A      N    41_A     0.202     0    0.023   0.142     0.878  100.000   98.810
LGA    V    42_A      V    42_A     0.660     0    0.044   1.155     3.324   95.238   84.898
LGA    E    43_A      E    43_A     0.290     0    0.051   0.128     0.935  100.000   95.767
LGA    G    44_A      G    44_A     0.385     0    0.014   0.014     0.385  100.000  100.000
LGA    K    45_A      K    45_A     0.156     0    0.026   0.742     4.692  100.000   77.566
LGA    R    46_A      R    46_A     0.313     0    0.016   0.128     1.101  100.000   92.338
LGA    G    47_A      G    47_A     0.361     0    0.016   0.016     0.378  100.000  100.000
LGA    L    48_A      L    48_A     0.407     0    0.031   0.050     0.519  100.000   98.810
LGA    I    49_A      I    49_A     0.395     0    0.033   0.063     0.473  100.000  100.000
LGA    H    50_A      H    50_A     0.557     0    0.022   0.121     0.945   90.476   90.476
LGA    V    51_A      V    51_A     0.552     0    0.029   0.040     0.617   92.857   91.837
LGA    V    52_A      V    52_A     0.809     0    0.015   0.057     1.123   90.476   87.891
LGA    L    53_A      L    53_A     0.599     0    0.025   0.077     1.025   95.238   91.726
LGA    V    54_A      V    54_A     0.191     0    0.078   0.093     0.448  100.000  100.000
LGA    E    55_A      E    55_A     0.246     0    0.022   0.175     0.392  100.000  100.000
LGA    K    56_A      K    56_A     0.318     0    0.013   0.892     4.457  100.000   85.132
LGA    Y    57_A      Y    57_A     0.302     0    0.574   0.561     2.316   91.190   87.778
LGA    G    58_A      G    58_A     2.405     0    0.134   0.134     3.130   57.381   57.381

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.033         12.966                 13.429           60.199   56.714

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.34    65.086    57.441     2.648

LGA_LOCAL      RMSD:   1.335  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.147  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.033  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.001160 * X  +   0.965681 * Y  +  -0.259730 * Z  + -22.069880
  Y_new =  -0.999946 * X  +   0.001559 * Y  +   0.010262 * Z  +  17.327181
  Z_new =   0.010314 * X  +   0.259728 * Y  +   0.965627 * Z  + -18.861273 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.571957 -0.010314  0.262755   [DEG:  -90.0665   -0.5910   15.0547 ]
ZXZ: -1.610284  0.262952  0.039691   [DEG:  -92.2625   15.0661    2.2741 ]
 
# END of job
