
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        2.78     2.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48       8_C - 55_C        1.99     2.84
  LCS_AVERAGE:     91.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      29_C - 50_C        0.95     3.21
  LONGEST_CONTINUOUS_SEGMENT:    22      30_C - 51_C        1.00     3.12
  LCS_AVERAGE:     38.18

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3    4   51      3    3    3    4    5    5    8    8    8   13   19   27   44   45   47   47   49   50   51   51 
LCS_GDT     T     7_C     T     7_C     14   47   51      4    5   12   27   37   42   43   44   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     K     8_C     K     8_C     20   48   51      4   15   35   39   41   43   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     I     9_C     I     9_C     20   48   51     14   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     L    10_C     L    10_C     20   48   51     17   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     P    11_C     P    11_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     C    12_C     C    12_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     P    13_C     P    13_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     R    14_C     R    14_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     C    15_C     C    15_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     N    16_C     N    16_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     S    17_C     S    17_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     M    18_C     M    18_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     E    19_C     E    19_C     20   48   51     18   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     T    20_C     T    20_C     20   48   51     18   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     K    21_C     K    21_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     F    22_C     F    22_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     C    23_C     C    23_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Y    24_C     Y    24_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Y    25_C     Y    25_C     20   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     N    26_C     N    26_C     20   48   51      4   28   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     N    27_C     N    27_C     20   48   51      5   13   36   39   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Y    28_C     Y    28_C     20   48   51      5   10   15   22   35   42   44   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     N    29_C     N    29_C     22   48   51      7   16   35   38   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     V    30_C     V    30_C     22   48   51     16   30   36   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     N    31_C     N    31_C     22   48   51     23   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Q    32_C     Q    32_C     22   48   51     16   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     P    33_C     P    33_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     R    34_C     R    34_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     H    35_C     H    35_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     F    36_C     F    36_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     C    37_C     C    37_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     K    38_C     K    38_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     A    39_C     A    39_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     C    40_C     C    40_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Q    41_C     Q    41_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     R    42_C     R    42_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     Y    43_C     Y    43_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     W    44_C     W    44_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     T    45_C     T    45_C     22   48   51     26   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     S    46_C     S    46_C     22   48   51     23   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     G    47_C     G    47_C     22   48   51      7   32   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     G    48_C     G    48_C     22   48   51     11   34   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     T    49_C     T    49_C     22   48   51      4   26   37   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     M    50_C     M    50_C     22   48   51      4   17   34   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     R    51_C     R    51_C     22   48   51      8   11   27   40   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     S    52_C     S    52_C     11   48   51      3   10   17   32   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     V    53_C     V    53_C     11   48   51      3   11   22   35   41   44   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     P    54_C     P    54_C     11   48   51      3    5    9   17   22   34   42   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     I    55_C     I    55_C     11   48   51      3   10   14   20   30   38   45   46   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_GDT     G    56_C     G    56_C      6   15   51      3    3    9   14   21   30   37   44   47   49   49   50   50   50   50   50   50   50   51   51 
LCS_AVERAGE  LCS_A:  76.43  (  38.18   91.12  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     26     34     37     40     41     44     45     46     47     49     49     50     50     50     50     50     50     50     51     51 
GDT PERCENT_AT  50.98  66.67  72.55  78.43  80.39  86.27  88.24  90.20  92.16  96.08  96.08  98.04  98.04  98.04  98.04  98.04  98.04  98.04 100.00 100.00
GDT RMS_LOCAL    0.30   0.54   0.72   0.98   0.99   1.40   1.49   1.61   1.81   2.17   2.17   2.31   2.31   2.31   2.31   2.31   2.31   2.31   2.78   2.78
GDT RMS_ALL_AT   3.33   3.26   3.15   3.02   3.22   2.91   2.90   2.91   2.86   2.85   2.85   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.78   2.78

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C    11.595     2    0.350   0.360    13.366    0.357    0.204
LGA    T     7_C      T     7_C     5.403     0    0.447   0.353     7.329   30.833   32.721
LGA    K     8_C      K     8_C     3.591     4    0.330   0.350     4.244   48.690   27.989
LGA    I     9_C      I     9_C     1.921     0    0.076   0.714     3.751   68.810   68.333
LGA    L    10_C      L    10_C     1.279     0    0.079   0.275     2.777   85.952   79.583
LGA    P    11_C      P    11_C     0.721     0    0.014   0.054     1.239   90.476   87.891
LGA    C    12_C      C    12_C     0.666     0    0.048   0.110     1.075   88.214   88.968
LGA    P    13_C      P    13_C     1.238     0    0.083   0.285     2.106   79.286   77.823
LGA    R    14_C      R    14_C     1.466     0    0.188   0.826     4.231   75.119   72.078
LGA    C    15_C      C    15_C     0.901     0    0.045   0.160     0.912   90.476   90.476
LGA    N    16_C      N    16_C     0.465     0    0.050   0.285     1.553   97.619   90.774
LGA    S    17_C      S    17_C     0.332     0    0.093   0.143     0.560   97.619   98.413
LGA    M    18_C      M    18_C     0.346     0    0.048   0.618     2.054   97.619   90.893
LGA    E    19_C      E    19_C     0.427     4    0.054   0.054     0.475  100.000   55.556
LGA    T    20_C      T    20_C     0.532     0    0.079   0.105     0.745   92.857   91.837
LGA    K    21_C      K    21_C     0.303     0    0.030   0.443     3.408   97.619   85.503
LGA    F    22_C      F    22_C     0.285     0    0.021   0.071     0.584  100.000   97.403
LGA    C    23_C      C    23_C     0.528     0    0.046   0.057     0.787   90.476   92.063
LGA    Y    24_C      Y    24_C     0.741     0    0.033   0.076     1.823   90.476   83.056
LGA    Y    25_C      Y    25_C     0.747     0    0.133   0.170     1.080   88.214   91.310
LGA    N    26_C      N    26_C     1.376     0    0.078   0.405     3.031   75.119   67.202
LGA    N    27_C      N    27_C     2.769     0    0.319   0.327     8.250   69.048   41.607
LGA    Y    28_C      Y    28_C     4.224     0    0.219   1.358     7.392   42.857   25.714
LGA    N    29_C      N    29_C     2.232     0    0.097   0.225     2.880   66.905   65.893
LGA    V    30_C      V    30_C     1.635     0    0.047   1.151     4.533   77.143   67.143
LGA    N    31_C      N    31_C     0.481     0    0.015   0.391     1.579   90.595   87.202
LGA    Q    32_C      Q    32_C     0.568     0    0.037   0.368     3.316   90.476   80.159
LGA    P    33_C      P    33_C     0.794     0    0.042   0.130     1.075   90.476   89.184
LGA    R    34_C      R    34_C     0.984     0    0.045   0.884     4.654   90.476   71.342
LGA    H    35_C      H    35_C     0.698     0    0.086   0.184     0.891   90.476   90.476
LGA    F    36_C      F    36_C     1.022     0    0.023   0.145     1.781   88.214   81.558
LGA    C    37_C      C    37_C     0.842     0    0.077   0.136     1.210   88.214   88.968
LGA    K    38_C      K    38_C     0.964     0    0.121   0.474     1.792   90.476   84.550
LGA    A    39_C      A    39_C     0.891     0    0.125   0.124     0.962   90.476   90.476
LGA    C    40_C      C    40_C     1.188     0    0.047   0.058     1.249   81.429   81.429
LGA    Q    41_C      Q    41_C     1.500     0    0.029   0.799     3.221   75.000   68.624
LGA    R    42_C      R    42_C     1.438     0    0.025   1.071     5.172   81.429   66.320
LGA    Y    43_C      Y    43_C     1.183     0    0.069   0.146     1.411   81.429   81.429
LGA    W    44_C      W    44_C     1.113     0    0.043   0.204     1.333   81.429   83.367
LGA    T    45_C      T    45_C     0.959     0    0.049   0.111     1.308   85.952   84.014
LGA    S    46_C      S    46_C     0.664     0    0.066   0.139     1.303   88.214   88.968
LGA    G    47_C      G    47_C     1.308     0    0.052   0.052     1.709   79.286   79.286
LGA    G    48_C      G    48_C     0.884     0    0.069   0.069     1.028   88.214   88.214
LGA    T    49_C      T    49_C     1.121     0    0.117   0.226     1.820   83.690   81.497
LGA    M    50_C      M    50_C     1.820     0    0.174   0.739     3.557   72.857   63.333
LGA    R    51_C      R    51_C     2.150     0    0.135   0.339     3.989   62.857   58.874
LGA    S    52_C      S    52_C     3.975     0    0.133   0.171     5.632   45.000   38.810
LGA    V    53_C      V    53_C     3.784     0    0.169   1.162     4.720   38.810   42.789
LGA    P    54_C      P    54_C     7.084     0    0.104   0.280     8.463   14.405   12.789
LGA    I    55_C      I    55_C     6.146     0    0.097   1.302     7.711   12.738   12.976
LGA    G    56_C      G    56_C     7.799     0    0.553   0.553     7.908    9.405    9.405

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     2.785          2.734                  2.871           75.173   70.127

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     46    1.61    83.333    87.262     2.694

LGA_LOCAL      RMSD:   1.607  Number of atoms:   46  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.908  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.785  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.595600 * X  +   0.550370 * Y  +  -0.585110 * Z  + -28.730898
  Y_new =  -0.774522 * X  +   0.586627 * Y  +  -0.236610 * Z  +  -7.894431
  Z_new =   0.213018 * X  +   0.594105 * Y  +   0.775669 * Z  +   6.881824 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.915252 -0.214663  0.653616   [DEG:  -52.4401  -12.2993   37.4495 ]
ZXZ: -1.186515  0.683022  0.344274   [DEG:  -67.9823   39.1343   19.7254 ]
 
# END of job
