
#######################################################
#                                                     #
#                        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   47 (  361),  selected   47 , name one
# Molecule2: number of CA atoms   79 (  632),  selected   47 , 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:    47       4_A - 50_A        2.80     2.80
  LCS_AVERAGE:     59.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      20_A - 50_A        1.87     3.44
  LCS_AVERAGE:     31.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      32_A - 50_A        0.70     4.23
  LCS_AVERAGE:     18.88

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   47
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     L     4_A     L     4_A     12   14   47      7    9   21   24   27   33   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L     5_A     L     5_A     12   14   47      7   11   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     C     6_A     C     6_A     12   14   47      7   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     P     7_A     P     7_A     12   14   47      9   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     N     8_A     N     8_A     12   14   47      5    9   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     C     9_A     C     9_A     12   14   47      5    8   18   24   31   34   38   41   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     Q    10_A     Q    10_A     12   14   47      3    9   16   24   27   33   38   41   42   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    11_A     V    11_A     12   14   47      7    9   18   24   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     G    12_A     G    12_A     12   14   47      7   15   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     M    13_A     M    13_A     12   14   47      9   16   21   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     R    14_A     R    14_A     12   14   47      7   16   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    15_A     E    15_A     12   14   47      5   16   21   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    16_A     V    16_A     10   14   47      6   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    17_A     E    17_A     10   14   47      7    9   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     R    18_A     R    18_A     10   14   47      7    9   16   22   25   32   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     R    19_A     R    19_A     10   14   47      7    9   12   14   24   29   33   36   41   45   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     G    20_A     G    20_A     10   31   47      7    9   12   22   29   32   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    21_A     V    21_A     10   31   47      7    9   16   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L    22_A     L    22_A     10   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     I    23_A     I    23_A     14   31   47      8   16   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     D    24_A     D    24_A     14   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    25_A     V    25_A     14   31   47      9   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     C    26_A     C    26_A     14   31   47      9   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     P    27_A     P    27_A     14   31   47      9   16   22   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     Q    28_A     Q    28_A     14   31   47      9   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     C    29_A     C    29_A     14   31   47      9   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     G    30_A     G    30_A     14   31   47      4   12   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     G    31_A     G    31_A     14   31   47      6   16   21   25   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    32_A     V    32_A     19   31   47      5   16   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     W    33_A     W    33_A     19   31   47      8   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L    34_A     L    34_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     D    35_A     D    35_A     19   31   47      6   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     K    36_A     K    36_A     19   31   47      5   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     G    37_A     G    37_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    38_A     E    38_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L    39_A     L    39_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    40_A     E    40_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     K    41_A     K    41_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L    42_A     L    42_A     19   31   47     12   20   23   26   31   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     L    43_A     L    43_A     19   31   47     12   20   23   26   30   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     A    44_A     A    44_A     19   31   47     12   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    45_A     E    45_A     19   31   47     12   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     A    46_A     A    46_A     19   31   47     12   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    47_A     E    47_A     19   31   47      8   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    48_A     E    48_A     19   31   47      8   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     V    49_A     V    49_A     19   31   47     10   20   23   26   29   34   38   43   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_GDT     E    50_A     E    50_A     19   31   47     10   20   23   26   29   32   37   42   44   46   47   47   47   47   47   47   47   47   47   47 
LCS_AVERAGE  LCS_A:  36.76  (  18.88   31.91   59.49 )

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     12     20     23     26     31     34     38     43     44     46     47     47     47     47     47     47     47     47     47     47 
GDT PERCENT_AT  15.19  25.32  29.11  32.91  39.24  43.04  48.10  54.43  55.70  58.23  59.49  59.49  59.49  59.49  59.49  59.49  59.49  59.49  59.49  59.49
GDT RMS_LOCAL    0.31   0.60   0.78   0.99   1.64   1.94   2.18   2.50   2.55   2.72   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_ALL_AT   4.50   4.42   4.46   4.33   3.64   3.03   2.92   2.82   2.83   2.81   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80

# Checking swapping
#   possible swapping detected:  D    35_A      D    35_A
#   possible swapping detected:  E    38_A      E    38_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     4_A      L     4_A     3.846     0    0.139   0.220     6.136   50.119   37.798
LGA    L     5_A      L     5_A     3.010     4    0.117   0.117     3.341   59.405   29.702
LGA    C     6_A      C     6_A     1.652     0    0.036   0.477     2.805   68.810   66.190
LGA    P     7_A      P     7_A     1.987     0    0.028   0.101     3.404   63.214   71.020
LGA    N     8_A      N     8_A     4.275     0    0.149   0.186     6.221   32.619   30.714
LGA    C     9_A      C     9_A     5.193     0    0.341   0.648     5.970   27.738   30.079
LGA    Q    10_A      Q    10_A     5.575     0    0.125   1.443     7.994   21.786   20.582
LGA    V    11_A      V    11_A     3.969     0    0.044   0.361     6.021   50.595   43.810
LGA    G    12_A      G    12_A     2.043     0    0.110   0.110     2.675   78.095   78.095
LGA    M    13_A      M    13_A     1.209     0    0.076   0.900     1.963   77.143   78.274
LGA    R    14_A      R    14_A     2.477     0    0.106   1.587    12.754   68.810   34.113
LGA    E    15_A      E    15_A     2.911     0    0.021   0.644     3.428   51.786   54.815
LGA    V    16_A      V    16_A     3.267     0    0.065   1.114     4.464   61.190   52.653
LGA    E    17_A      E    17_A     1.472     0    0.015   0.177     2.753   67.024   75.185
LGA    R    18_A      R    18_A     3.914     3    0.055   0.577     6.761   43.690   24.372
LGA    R    19_A      R    19_A     5.408     5    0.043   0.407     8.417   27.619   12.035
LGA    G    20_A      G    20_A     3.904     0    0.033   0.033     4.073   45.119   45.119
LGA    V    21_A      V    21_A     2.603     0    0.089   0.089     3.843   63.214   59.728
LGA    L    22_A      L    22_A     1.190     0    0.035   0.956     4.904   79.286   68.869
LGA    I    23_A      I    23_A     2.596     0    0.093   1.024     3.883   62.976   58.333
LGA    D    24_A      D    24_A     2.332     0    0.038   0.352     3.005   62.857   63.988
LGA    V    25_A      V    25_A     2.217     0    0.080   0.151     2.505   68.810   65.986
LGA    C    26_A      C    26_A     1.401     0    0.062   0.220     2.698   75.000   70.317
LGA    P    27_A      P    27_A     1.311     0    0.063   0.408     1.954   77.143   79.048
LGA    Q    28_A      Q    28_A     2.362     0    0.218   0.778     6.082   64.881   50.688
LGA    C    29_A      C    29_A     3.314     0    0.716   0.619     4.317   48.571   51.508
LGA    G    30_A      G    30_A     3.227     0    0.036   0.036     3.371   51.786   51.786
LGA    G    31_A      G    31_A     2.081     0    0.057   0.057     2.463   70.952   70.952
LGA    V    32_A      V    32_A     1.973     0    0.085   0.108     2.732   72.857   67.211
LGA    W    33_A      W    33_A     1.817     0    0.081   1.514     6.572   72.857   58.605
LGA    L    34_A      L    34_A     2.163     0    0.072   0.266     2.262   64.762   67.857
LGA    D    35_A      D    35_A     2.257     0    0.114   1.242     6.017   66.786   52.202
LGA    K    36_A      K    36_A     2.624     0    0.020   0.684     6.119   62.976   46.296
LGA    G    37_A      G    37_A     2.159     0    0.022   0.022     2.300   68.810   68.810
LGA    E    38_A      E    38_A     1.062     0    0.047   1.201     3.527   83.810   72.910
LGA    L    39_A      L    39_A     1.089     0    0.035   0.049     1.892   85.952   79.405
LGA    E    40_A      E    40_A     0.518     0    0.023   0.709     3.325   95.238   77.831
LGA    K    41_A      K    41_A     0.559     0    0.058   0.215     2.826   92.857   82.963
LGA    L    42_A      L    42_A     0.717     0    0.014   0.143     1.683   88.333   83.810
LGA    L    43_A      L    43_A     1.345     0    0.036   0.098     1.835   79.286   78.214
LGA    A    44_A      A    44_A     1.438     0    0.076   0.080     2.285   75.119   76.381
LGA    E    45_A      E    45_A     1.675     0    0.016   1.210     4.755   70.952   65.820
LGA    A    46_A      A    46_A     2.409     0    0.077   0.082     3.068   61.190   61.905
LGA    E    47_A      E    47_A     3.188     0    0.033   0.425     4.502   50.119   44.392
LGA    E    48_A      E    48_A     3.325     0    0.065   1.117     4.334   48.333   46.349
LGA    V    49_A      V    49_A     3.729     0    0.099   0.107     4.703   40.476   44.626
LGA    E    50_A      E    50_A     4.425     0    0.563   0.867     6.178   37.262   29.735

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       47     188    188  100.00     349    349  100.00                79
SUMMARY(RMSD_GDC):     2.803          2.795                  3.405           37.193   33.938

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47   79    4.0     43    2.50    43.038    42.273     1.656

LGA_LOCAL      RMSD:   2.497  Number of atoms:   43  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.824  Number of assigned atoms:   47 
Std_ASGN_ATOMS RMSD:   2.803  Standard rmsd on all 47 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.040701 * X  +  -0.990599 * Y  +   0.130602 * Z  + -32.159054
  Y_new =  -0.978496 * X  +   0.065970 * Y  +   0.195431 * Z  +  -9.727664
  Z_new =  -0.202209 * X  +  -0.119839 * Y  +  -0.971983 * Z  +  11.249002 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.612368  0.203613 -3.018918   [DEG:  -92.3819   11.6662 -172.9713 ]
ZXZ:  2.552476  2.904320 -2.105793   [DEG:  146.2461  166.4052 -120.6530 ]
 
# END of job
