
#######################################################
#                                                     #
#                        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   59 (  440),  selected   59 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   59 , 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:    59       5_A - 63_A        1.73     1.73
  LCS_AVERAGE:     93.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    59       5_A - 63_A        1.73     1.73
  LCS_AVERAGE:     93.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      13_A - 39_A        1.00     2.37
  LCS_AVERAGE:     34.44

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   59
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     C     5_A     C     5_A     21   59   59      8   17   33   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     D     6_A     D     6_A     21   59   59      8   12   34   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K     7_A     K     7_A     21   59   59      9   22   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     E     8_A     E     8_A     21   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C     9_A     C     9_A     21   59   59      8   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     N    10_A     N    10_A     21   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     R    11_A     R    11_A     21   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     R    12_A     R    12_A     21   59   59      8   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    13_A     C    13_A     27   59   59      8   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     S    14_A     S    14_A     27   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    15_A     K    15_A     27   59   59      4    6   19   43   55   56   56   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     A    16_A     A    16_A     27   59   59      4   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     S    17_A     S    17_A     27   59   59      6   23   40   54   55   56   56   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     A    18_A     A    18_A     27   59   59      3    3   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     H    19_A     H    19_A     27   59   59      3   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     D    20_A     D    20_A     27   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     R    21_A     R    21_A     27   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    22_A     C    22_A     27   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     L    23_A     L    23_A     27   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    24_A     K    24_A     27   59   59      5   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     Y    25_A     Y    25_A     27   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    26_A     C    26_A     27   59   59      5   21   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     G    27_A     G    27_A     27   59   59      4   19   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     I    28_A     I    28_A     27   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    29_A     C    29_A     27   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    30_A     C    30_A     27   59   59      5   19   40   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     E    31_A     E    31_A     27   59   59      4   14   34   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    32_A     K    32_A     27   59   59      4   21   35   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    33_A     C    33_A     27   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     N    34_A     N    34_A     27   59   59      4   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    35_A     C    35_A     27   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     V    36_A     V    36_A     27   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     P    37_A     P    37_A     27   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     P    38_A     P    38_A     27   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     G    39_A     G    39_A     27   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     T    40_A     T    40_A      8   59   59      3    6   14   33   46   54   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     Y    41_A     Y    41_A      8   59   59      3    6   17   26   41   51   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     G    42_A     G    42_A     14   59   59      4    5   17   26   41   51   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     N    43_A     N    43_A     17   59   59      4   20   39   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     E    44_A     E    44_A     17   59   59      9   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     D    45_A     D    45_A     17   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     S    46_A     S    46_A     17   59   59      4   17   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    47_A     C    47_A     17   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     P    48_A     P    48_A     17   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    49_A     C    49_A     17   59   59      4   23   36   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     Y    50_A     Y    50_A     17   59   59      6   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     A    51_A     A    51_A     17   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     N    52_A     N    52_A     17   59   59     10   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     L    53_A     L    53_A     17   59   59      3   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    54_A     K    54_A     17   59   59      3   16   35   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     N    55_A     N    55_A     17   59   59      5   20   35   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     S    56_A     S    56_A     17   59   59      5    9   25   47   54   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    57_A     K    57_A     17   59   59      9   20   35   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     G    58_A     G    58_A     17   59   59      5   20   35   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     G    59_A     G    59_A     17   59   59      5   21   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     H    60_A     H    60_A     16   59   59      5   21   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     K    61_A     K    61_A     16   59   59      4   15   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     C    62_A     C    62_A     16   59   59      6   23   40   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_GDT     P    63_A     P    63_A     16   59   59      7   23   41   54   55   56   57   59   59   59   59   59   59   59   59   59   59   59   59   59 
LCS_AVERAGE  LCS_A:  73.91  (  34.44   93.65   93.65 )

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     10     23     41     54     55     56     57     59     59     59     59     59     59     59     59     59     59     59     59     59 
GDT PERCENT_AT  15.87  36.51  65.08  85.71  87.30  88.89  90.48  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65  93.65
GDT RMS_LOCAL    0.32   0.68   1.11   1.35   1.38   1.43   1.67   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73
GDT RMS_ALL_AT   2.03   2.12   1.82   1.76   1.77   1.77   1.74   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73

# Checking swapping
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    C     5_A      C     5_A     1.797     0    0.106   0.216     2.369   72.857   71.508
LGA    D     6_A      D     6_A     1.676     0    0.017   0.640     3.592   77.143   70.298
LGA    K     7_A      K     7_A     0.563     0    0.050   0.991     3.775   92.857   78.677
LGA    E     8_A      E     8_A     0.770     0    0.068   0.706     3.640   85.952   74.286
LGA    C     9_A      C     9_A     1.233     0    0.032   0.057     1.905   81.429   80.000
LGA    N    10_A      N    10_A     0.472     0    0.107   0.656     2.107   92.857   89.643
LGA    R    11_A      R    11_A     1.015     0    0.030   1.133     6.914   83.690   51.948
LGA    R    12_A      R    12_A     1.428     0    0.065   1.321     6.458   79.286   62.121
LGA    C    13_A      C    13_A     1.136     0    0.173   0.204     3.174   83.690   77.698
LGA    S    14_A      S    14_A     1.273     0    0.085   0.659     3.370   73.452   72.381
LGA    K    15_A      K    15_A     3.251     0    0.040   1.002     4.759   55.476   51.376
LGA    A    16_A      A    16_A     1.901     0    0.024   0.029     2.205   66.786   69.714
LGA    S    17_A      S    17_A     2.522     0    0.048   0.460     4.533   60.952   55.397
LGA    A    18_A      A    18_A     1.806     0    0.133   0.132     2.058   70.833   71.238
LGA    H    19_A      H    19_A     1.769     0    0.080   0.335     3.200   70.833   67.381
LGA    D    20_A      D    20_A     1.464     0    0.154   0.161     1.962   79.286   76.071
LGA    R    21_A      R    21_A     1.357     0    0.048   0.517     5.398   83.690   61.039
LGA    C    22_A      C    22_A     0.968     0    0.119   0.177     1.265   85.952   87.460
LGA    L    23_A      L    23_A     0.787     0    0.111   1.469     4.277   92.857   74.643
LGA    K    24_A      K    24_A     1.741     0    0.077   0.460     4.501   72.857   60.741
LGA    Y    25_A      Y    25_A     1.803     0    0.032   0.584     2.354   70.833   69.484
LGA    C    26_A      C    26_A     1.608     0    0.063   0.210     1.976   72.857   74.286
LGA    G    27_A      G    27_A     1.694     0    0.126   0.126     2.393   70.833   70.833
LGA    I    28_A      I    28_A     1.362     0    0.045   0.675     3.826   81.429   73.452
LGA    C    29_A      C    29_A     1.518     0    0.035   0.656     1.620   79.286   80.079
LGA    C    30_A      C    30_A     1.601     0    0.052   0.089     2.461   72.857   70.159
LGA    E    31_A      E    31_A     1.938     0    0.019   0.649     3.736   70.833   61.058
LGA    K    32_A      K    32_A     1.962     0    0.023   1.015     6.600   70.833   52.646
LGA    C    33_A      C    33_A     1.105     0    0.622   0.539     3.731   69.762   69.603
LGA    N    34_A      N    34_A     1.260     0    0.217   0.714     3.889   83.690   71.726
LGA    C    35_A      C    35_A     1.429     0    0.114   0.841     1.905   81.429   78.571
LGA    V    36_A      V    36_A     0.302     0    0.137   0.182     1.417   97.619   94.626
LGA    P    37_A      P    37_A     0.299     0    0.040   0.269     0.739  100.000   98.639
LGA    P    38_A      P    38_A     0.961     0    0.055   0.108     1.064   88.214   87.891
LGA    G    39_A      G    39_A     1.580     0    0.154   0.154     2.595   69.048   69.048
LGA    T    40_A      T    40_A     4.128     0    0.562   0.505     5.259   39.405   36.939
LGA    Y    41_A      Y    41_A     4.525     0    0.133   1.260     5.513   35.714   32.103
LGA    G    42_A      G    42_A     4.344     0    0.593   0.593     5.506   31.786   31.786
LGA    N    43_A      N    43_A     1.427     0    0.237   0.331     2.044   75.119   81.667
LGA    E    44_A      E    44_A     0.622     0    0.153   0.677     3.496   90.476   72.487
LGA    D    45_A      D    45_A     0.788     0    0.176   0.723     3.376   88.214   76.905
LGA    S    46_A      S    46_A     1.274     0    0.119   0.237     1.714   83.690   80.079
LGA    C    47_A      C    47_A     0.720     0    0.027   0.451     2.692   90.476   83.413
LGA    P    48_A      P    48_A     0.639     0    0.101   0.344     1.029   88.214   91.905
LGA    C    49_A      C    49_A     1.600     0    0.037   0.197     2.908   77.143   71.746
LGA    Y    50_A      Y    50_A     0.682     0    0.047   0.211     1.751   90.476   85.278
LGA    A    51_A      A    51_A     0.655     0    0.124   0.141     1.106   88.214   88.667
LGA    N    52_A      N    52_A     1.025     0    0.088   0.317     2.141   88.214   82.738
LGA    L    53_A      L    53_A     1.144     0    0.126   0.787     2.505   81.429   79.524
LGA    K    54_A      K    54_A     1.413     0    0.089   0.992     2.489   81.429   76.984
LGA    N    55_A      N    55_A     1.617     0    0.009   0.267     2.280   70.952   71.905
LGA    S    56_A      S    56_A     2.966     0    0.077   0.662     5.689   55.357   48.810
LGA    K    57_A      K    57_A     1.606     0    0.166   0.544     3.430   72.857   71.323
LGA    G    58_A      G    58_A     1.568     0    0.037   0.037     1.568   77.143   77.143
LGA    G    59_A      G    59_A     0.781     0    0.020   0.020     1.037   88.214   88.214
LGA    H    60_A      H    60_A     0.745     0    0.141   1.357     7.429   90.476   58.429
LGA    K    61_A      K    61_A     1.414     0    0.044   0.757     1.876   79.405   79.577
LGA    C    62_A      C    62_A     1.900     0    0.119   0.173     2.091   70.833   68.810
LGA    P    63_A      P    63_A     1.632     0    0.404   0.414     2.178   70.833   72.925

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       59     236    236  100.00     440    440  100.00                63
SUMMARY(RMSD_GDC):     1.734          1.781                  2.358           72.196   67.223

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   59   63    4.0     59    1.73    77.381    85.561     3.217

LGA_LOCAL      RMSD:   1.734  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.734  Number of assigned atoms:   59 
Std_ASGN_ATOMS RMSD:   1.734  Standard rmsd on all 59 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.969918 * X  +   0.128972 * Y  +  -0.206459 * Z  +  31.035286
  Y_new =   0.169532 * X  +   0.966506 * Y  +  -0.192680 * Z  +   7.572976
  Z_new =   0.174693 * X  +  -0.221885 * Y  +  -0.959296 * Z  + -11.906572 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.968550 -0.175594 -2.914290   [DEG:  170.0854  -10.0608 -166.9765 ]
ZXZ: -0.819906  2.855296  2.474635   [DEG:  -46.9772  163.5964  141.7861 ]
 
# END of job
