
#######################################################
#                                                     #
#                        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   30 (  233),  selected   30 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   30 , 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:    23      47_A - 69_A        4.74    11.06
  LCS_AVERAGE:     35.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      40_A - 53_A        0.60    20.12
  LCS_AVERAGE:     21.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      40_A - 53_A        0.60    20.12
  LCS_AVERAGE:     16.94

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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     Q    40_A     Q    40_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   16   17   19   20   21   21   22 
LCS_GDT     A    41_A     A    41_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   16   17   18   19   19   21   21 
LCS_GDT     V    42_A     V    42_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   16   16   18   19   19   19   20 
LCS_GDT     K    43_A     K    43_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   16   17   19   20   21   21   22 
LCS_GDT     E    44_A     E    44_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   17   18   19   20   21   22   23 
LCS_GDT     I    45_A     I    45_A     14   14   18     13   13   14   14   14   14   14   14   14   14   15   16   16   16   17   19   20   21   21   22 
LCS_GDT     C    46_A     C    46_A     14   14   19     13   13   14   14   14   14   14   14   14   14   15   16   16   16   18   19   20   21   22   23 
LCS_GDT     Y    47_A     Y    47_A     14   14   23     13   13   14   14   14   14   14   14   14   14   15   16   18   20   22   23   23   23   23   23 
LCS_GDT     E    48_A     E    48_A     14   14   23     13   13   14   14   14   14   14   14   14   14   15   16   20   20   22   23   23   23   23   23 
LCS_GDT     V    49_A     V    49_A     14   14   23     13   13   14   14   14   14   14   14   14   14   15   16   17   18   22   23   23   23   23   23 
LCS_GDT     A    50_A     A    50_A     14   14   23     13   13   14   14   14   14   14   14   14   16   18   20   20   20   22   23   23   23   23   23 
LCS_GDT     L    51_A     L    51_A     14   14   23     13   13   14   14   14   14   15   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     A    52_A     A    52_A     14   14   23     13   13   14   14   14   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     D    53_A     D    53_A     14   14   23      3    7   14   14   14   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     F    54_A     F    54_A      3    5   23      3    5    6   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     R    55_A     R    55_A      3    5   23      3    5    6    8   11   13   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     H    56_A     H    56_A      3   13   23      3    4    5   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     G    57_A     G    57_A      9   13   23      3    8    9   10   11   12   15   16   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     R    58_A     R    58_A      9   13   23      3    4    9   10   12   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     A    59_A     A    59_A      9   13   23      7    8    9   10   12   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     E    60_A     E    60_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     I    61_A     I    61_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     E    62_A     E    62_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     A    63_A     A    63_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     L    64_A     L    64_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     A    65_A     A    65_A      9   13   23      7    8    9   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     A    66_A     A    66_A      6   13   23      5    5    6   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     L    67_A     L    67_A      6   13   23      5    5    6   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     K    68_A     K    68_A      6   13   23      5    5    6   10   13   15   16   17   18   19   19   20   20   20   22   23   23   23   23   23 
LCS_GDT     M    69_A     M    69_A      6   10   23      2    3    6    7    9   14   16   17   18   19   19   20   20   20   21   23   23   23   23   23 
LCS_AVERAGE  LCS_A:  24.61  (  16.94   21.04   35.85 )

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     13     13     14     14     14     15     16     17     18     19     19     20     20     20     22     23     23     23     23     23 
GDT PERCENT_AT  21.31  21.31  22.95  22.95  22.95  24.59  26.23  27.87  29.51  31.15  31.15  32.79  32.79  32.79  36.07  37.70  37.70  37.70  37.70  37.70
GDT RMS_LOCAL    0.26   0.26   0.60   0.60   0.60   2.10   2.23   2.36   2.56   2.89   2.89   3.43   3.43   3.43   4.63   4.74   4.74   4.74   4.74   4.74
GDT RMS_ALL_AT  20.24  20.24  20.12  20.12  20.12  14.07  14.05  14.26  14.24  13.28  13.28  12.49  12.49  12.49  10.73  11.06  11.06  11.06  11.06  11.06

# Checking swapping
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    60_A      E    60_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    40_A      Q    40_A    33.670     0    0.018   1.226    36.332    0.000    0.000
LGA    A    41_A      A    41_A    30.810     0    0.087   0.090    32.539    0.000    0.000
LGA    V    42_A      V    42_A    31.486     0    0.077   0.135    35.994    0.000    0.000
LGA    K    43_A      K    43_A    28.103     0    0.087   0.837    35.141    0.000    0.000
LGA    E    44_A      E    44_A    22.427     0    0.138   1.049    25.003    0.000    0.000
LGA    I    45_A      I    45_A    21.322     0    0.062   0.089    27.511    0.000    0.000
LGA    C    46_A      C    46_A    20.773     0    0.035   0.754    24.523    0.000    0.000
LGA    Y    47_A      Y    47_A    16.895     0    0.068   1.378    18.764    0.000    0.000
LGA    E    48_A      E    48_A    11.463     0    0.039   1.049    14.197    1.786    0.794
LGA    V    49_A      V    49_A    11.486     0    0.025   0.051    15.760    1.190    0.680
LGA    A    50_A      A    50_A    11.183     0    0.024   0.023    13.872    1.548    1.238
LGA    L    51_A      L    51_A     7.406     0    0.267   1.329    10.589   18.929   10.774
LGA    A    52_A      A    52_A     1.904     0    0.249   0.244     4.522   67.619   60.381
LGA    D    53_A      D    53_A     2.404     0    0.332   1.039     7.299   63.095   43.036
LGA    F    54_A      F    54_A     0.826     0    0.295   1.210     6.385   75.476   56.970
LGA    R    55_A      R    55_A     3.575     0    0.066   1.350    11.759   53.810   23.983
LGA    H    56_A      H    56_A     0.837     0    0.650   1.139     7.119   73.690   45.571
LGA    G    57_A      G    57_A     5.091     0    0.649   0.649     5.091   39.167   39.167
LGA    R    58_A      R    58_A     3.499     0    0.328   0.836     9.443   50.357   26.797
LGA    A    59_A      A    59_A     3.163     0    0.036   0.034     3.887   57.738   54.857
LGA    E    60_A      E    60_A     1.689     0    0.031   1.374     5.278   72.976   54.974
LGA    I    61_A      I    61_A     2.656     0    0.079   0.994     6.904   66.905   51.905
LGA    E    62_A      E    62_A     0.948     0    0.075   0.863     3.210   86.071   78.148
LGA    A    63_A      A    63_A     1.491     0    0.078   0.088     3.009   71.667   73.619
LGA    L    64_A      L    64_A     2.912     0    0.099   0.537     4.872   57.500   50.595
LGA    A    65_A      A    65_A     2.452     0    0.087   0.097     2.858   64.881   63.333
LGA    A    66_A      A    66_A     2.105     0    0.182   0.202     2.676   68.810   66.476
LGA    L    67_A      L    67_A     1.794     0    0.026   0.873     3.906   75.000   66.250
LGA    K    68_A      K    68_A     1.173     0    0.087   0.612     3.540   71.667   65.556
LGA    M    69_A      M    69_A     3.464     0    0.607   1.004     6.948   45.833   43.512

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     233    233  100.00                61
SUMMARY(RMSD_GDC):     8.713          8.631                  9.255           19.438   16.043

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   30   61    4.0     17    2.36    27.459    25.730     0.692

LGA_LOCAL      RMSD:   2.356  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.262  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:   8.713  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.045806 * X  +   0.157218 * Y  +  -0.986501 * Z  +   6.268578
  Y_new =   0.023255 * X  +  -0.987438 * Y  +  -0.156287 * Z  +  65.890320
  Z_new =  -0.998680 * X  +  -0.015783 * Y  +  -0.048887 * Z  + -35.292202 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.469781  1.519403 -2.829318   [DEG:   26.9165   87.0554 -162.1080 ]
ZXZ: -1.413677  1.619703 -1.586598   [DEG:  -80.9977   92.8021  -90.9054 ]
 
# END of job
