
#######################################################
#                                                     #
#                        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   38 (  302),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        3.17     3.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.98     3.43
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.84     3.69
  LCS_AVERAGE:     82.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.81     3.81
  LCS_AVERAGE:     71.80

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     2_C     A     2_B      4    4   37      0    3    4    4    4    4    4    5   29   30   31   35   36   36   37   37   37   37   37   37 
LCS_GDT     E     3_C     E     3_B      4    4   37      1    3    4    4    4    4    4   25   29   30   31   33   36   36   37   37   37   37   37   37 
LCS_GDT     A     4_C     A     4_B      4    4   37      3    3    4    4   12   21   22   25   29   30   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     E     5_C     E     5_B      4   33   37      3    3    4    4    5    6    7   17   18   24   31   35   36   36   37   37   37   37   37   37 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    5    9   25   30   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     E     7_C     E     7_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     K     8_C     K     8_B     31   33   37     11   22   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     D     9_C     D     9_B     31   33   37     11   21   28   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     11   25   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    11_C     L    11_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     R    12_C     R    12_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     T    13_C     T    13_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     V    15_C     V    15_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     V    16_C     V    16_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     R    17_C     R    17_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    18_C     L    18_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     A    20_C     A    20_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     E    21_C     E    21_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     K    22_C     K    22_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     A    23_C     A    23_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     D    24_C     D    24_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    25_C     L    25_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    26_C     L    26_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     G    27_C     G    27_B     31   33   37     17   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     I    28_C     I    28_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     V    29_C     V    29_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     S    30_C     S    30_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     E    31_C     E    31_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    32_C     L    32_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    34_C     L    34_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     K    35_C     K    35_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     L    36_C     L    36_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     N    37_C     N    37_B     31   33   37     14   26   29   31   31   31   31   32   32   32   33   35   36   36   37   37   37   37   37   37 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    6    9   16   20   30   32   36   37   37   37   37   37   37 
LCS_AVERAGE  LCS_A:  84.88  (  71.80   82.83  100.00 )

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     17     26     29     31     31     31     31     32     32     32     33     35     36     36     37     37     37     37     37     37 
GDT PERCENT_AT  45.95  70.27  78.38  83.78  83.78  83.78  83.78  86.49  86.49  86.49  89.19  94.59  97.30  97.30 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.56   0.68   0.81   0.81   0.81   0.81   1.23   1.23   1.23   1.93   2.63   2.87   2.87   3.17   3.17   3.17   3.17   3.17   3.17
GDT RMS_ALL_AT   4.01   3.74   3.81   3.81   3.81   3.81   3.81   3.66   3.66   3.66   3.40   3.21   3.20   3.20   3.17   3.17   3.17   3.17   3.17   3.17

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  E     7_C      E     7_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B     9.382     0    0.535   0.545    11.706    1.071    0.857
LGA    E     3_C      E     3_B    10.461     0    0.055   0.891    13.242    0.595    0.265
LGA    A     4_C      A     4_B     9.367     0    0.589   0.562    10.316    0.833    0.667
LGA    E     5_C      E     5_B     9.537     0    0.602   0.876    14.292    4.762    2.116
LGA    Q     6_C      Q     6_B     4.938     0    0.590   1.289    10.669   32.976   17.778
LGA    E     7_C      E     7_B     1.049     0    0.584   0.981     9.982   88.333   47.354
LGA    K     8_C      K     8_B     1.242     0    0.084   1.464     7.879   85.952   59.048
LGA    D     9_C      D     9_B     2.095     0    0.043   1.139     6.684   70.833   50.774
LGA    Q    10_C      Q    10_B     1.804     0    0.056   1.066     3.691   77.143   67.143
LGA    L    11_C      L    11_B     0.720     0    0.039   1.418     5.469   95.238   71.905
LGA    R    12_C      R    12_B     0.854     0    0.036   1.609     7.969   90.476   57.489
LGA    T    13_C      T    13_B     1.212     0    0.041   0.244     2.276   88.214   79.320
LGA    Q    14_C      Q    14_B     0.865     0    0.037   0.675     3.118   90.476   73.862
LGA    V    15_C      V    15_B     0.443     0    0.030   0.102     1.161  100.000   94.626
LGA    V    16_C      V    16_B     0.339     0    0.030   1.070     3.000  100.000   86.395
LGA    R    17_C      R    17_B     0.694     0    0.026   1.105     6.637   90.476   61.602
LGA    L    18_C      L    18_B     0.711     0    0.034   0.920     2.720   90.476   85.179
LGA    Q    19_C      Q    19_B     0.398     0    0.025   0.720     3.293  100.000   78.571
LGA    A    20_C      A    20_B     0.503     0    0.031   0.037     0.847   92.857   92.381
LGA    E    21_C      E    21_B     0.989     0    0.031   1.190     4.032   88.214   74.180
LGA    K    22_C      K    22_B     0.935     0    0.027   1.005     4.230   90.476   74.709
LGA    A    23_C      A    23_B     0.598     0    0.041   0.046     0.694   90.476   92.381
LGA    D    24_C      D    24_B     0.766     0    0.026   0.237     1.553   90.476   88.274
LGA    L    25_C      L    25_B     1.069     0    0.037   0.169     1.898   88.214   82.679
LGA    L    26_C      L    26_B     0.727     0    0.043   1.397     4.182   90.476   74.583
LGA    G    27_C      G    27_B     0.332     0    0.030   0.030     0.390  100.000  100.000
LGA    I    28_C      I    28_B     0.359     0    0.046   1.428     4.242  100.000   82.381
LGA    V    29_C      V    29_B     0.154     0    0.029   1.212     2.624  100.000   88.844
LGA    S    30_C      S    30_B     0.391     0    0.033   0.668     2.297  100.000   94.127
LGA    E    31_C      E    31_B     0.534     0    0.048   1.057     5.844   97.619   68.042
LGA    L    32_C      L    32_B     0.217     0    0.034   1.056     2.508  100.000   90.238
LGA    Q    33_C      Q    33_B     0.390     0    0.060   0.980     3.494   95.238   86.085
LGA    L    34_C      L    34_B     0.681     0    0.078   0.160     1.322   90.476   87.083
LGA    K    35_C      K    35_B     0.887     0    0.063   1.194     6.081   90.476   72.487
LGA    L    36_C      L    36_B     1.103     0    0.171   1.387     2.846   81.548   76.548
LGA    N    37_C      N    37_B     1.033     0    0.481   1.301     4.429   63.095   55.952
LGA    S    38_C      S    38_B     8.376     0    0.605   0.905    10.894    6.667    4.444

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     3.172          3.145                  4.100           77.410   65.415

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.23    85.135    84.898     2.398

LGA_LOCAL      RMSD:   1.234  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.658  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.172  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.451310 * X  +  -0.544716 * Y  +  -0.706826 * Z  +  -8.704782
  Y_new =   0.502185 * X  +  -0.499720 * Y  +   0.705755 * Z  +  49.005547
  Z_new =  -0.737652 * X  +  -0.673472 * Y  +   0.048020 * Z  + -47.852257 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.838704  0.829586 -1.499615   [DEG:   48.0542   47.5318  -85.9216 ]
ZXZ: -2.355436  1.522758 -2.310744   [DEG: -134.9565   87.2476 -132.3959 ]
 
# END of job
