
#######################################################
#                                                     #
#                        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        2.11     2.11
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.54     2.14
  LCS_AVERAGE:     98.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       7_C - 52_C        0.96     2.24
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.85     2.21
  LCS_AVERAGE:     84.62

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   49   51      0    3    3    4    5    6    7    8    8   25   33   42   48   50   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     46   50   51      3    5   13   29   45   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   50   51      5   34   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   50   51     17   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   50   51     10   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   50   51     25   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   50   51     17   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   50   51     17   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   50   51     14   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   50   51     26   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   50   51     29   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   50   51     21   41   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   50   51      3   38   44   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   50   51      3   10   31   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   50   51      4   29   41   45   46   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     12   50   51      3    4    6   18   33   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     12   50   51      4    8   16   31   43   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     12   50   51      3    8   15   25   41   47   49   50   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  94.21  (  84.62   98.00  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     29     41     44     45     46     47     49     50     50     50     50     50     50     50     51     51     51     51     51     51 
GDT PERCENT_AT  56.86  80.39  86.27  88.24  90.20  92.16  96.08  98.04  98.04  98.04  98.04  98.04  98.04  98.04 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.51   0.64   0.79   0.85   1.22   1.41   1.54   1.54   1.54   1.54   1.54   1.54   1.54   2.11   2.11   2.11   2.11   2.11   2.11
GDT RMS_ALL_AT   2.34   2.29   2.29   2.21   2.21   2.18   2.17   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.11   2.11   2.11   2.11   2.11   2.11

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_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    10.649     2    0.308   0.314    12.805    1.548    0.884
LGA    T     7_C      T     7_C     4.411     0    0.680   0.590     6.419   33.690   35.238
LGA    K     8_C      K     8_C     2.455     4    0.236   0.250     2.623   64.881   36.931
LGA    I     9_C      I     9_C     1.344     0    0.108   0.733     3.540   77.143   74.583
LGA    L    10_C      L    10_C     1.056     0    0.060   0.235     2.307   85.952   83.869
LGA    P    11_C      P    11_C     0.529     0    0.025   0.055     0.928   90.476   90.476
LGA    C    12_C      C    12_C     0.771     0    0.054   0.096     1.200   88.214   87.460
LGA    P    13_C      P    13_C     1.081     0    0.067   0.292     1.807   83.690   82.789
LGA    R    14_C      R    14_C     1.356     0    0.177   1.009     3.761   77.262   74.113
LGA    C    15_C      C    15_C     0.993     0    0.068   0.127     1.306   88.214   85.952
LGA    N    16_C      N    16_C     0.688     0    0.061   0.262     1.274   90.476   87.083
LGA    S    17_C      S    17_C     0.788     0    0.094   0.146     0.927   90.476   90.476
LGA    M    18_C      M    18_C     0.444     0    0.047   0.602     1.550   95.238   91.845
LGA    E    19_C      E    19_C     0.750     4    0.047   0.046     0.870   90.476   50.265
LGA    T    20_C      T    20_C     0.767     0    0.072   0.093     1.022   90.476   89.184
LGA    K    21_C      K    21_C     0.653     0    0.011   0.553     1.426   90.476   88.466
LGA    F    22_C      F    22_C     0.620     0    0.030   0.101     0.667   92.857   91.342
LGA    C    23_C      C    23_C     0.639     0    0.047   0.063     0.754   90.476   90.476
LGA    Y    24_C      Y    24_C     0.621     0    0.014   0.051     1.599   90.476   85.238
LGA    Y    25_C      Y    25_C     0.374     0    0.039   0.064     0.740  100.000   96.032
LGA    N    26_C      N    26_C     0.651     0    0.075   0.489     2.458   90.476   85.000
LGA    N    27_C      N    27_C     1.060     0    0.014   0.285     2.309   88.214   81.667
LGA    Y    28_C      Y    28_C     0.921     0    0.070   0.102     2.814   88.214   74.008
LGA    N    29_C      N    29_C     0.412     0    0.049   0.171     0.872  100.000   97.619
LGA    V    30_C      V    30_C     0.678     0    0.052   1.142     3.318   90.476   82.177
LGA    N    31_C      N    31_C     0.722     0    0.016   0.423     1.038   90.476   91.726
LGA    Q    32_C      Q    32_C     0.462     0    0.025   0.874     4.023   95.238   81.429
LGA    P    33_C      P    33_C     0.660     0    0.033   0.036     0.742   90.476   90.476
LGA    R    34_C      R    34_C     0.779     0    0.020   0.866     3.929   90.476   74.675
LGA    H    35_C      H    35_C     0.656     0    0.080   0.209     0.929   90.476   90.476
LGA    F    36_C      F    36_C     1.146     0    0.043   0.196     1.949   81.429   79.091
LGA    C    37_C      C    37_C     1.055     0    0.075   0.154     1.555   79.286   80.000
LGA    K    38_C      K    38_C     0.937     0    0.125   0.477     1.596   90.476   85.503
LGA    A    39_C      A    39_C     0.958     0    0.078   0.076     1.023   88.214   88.667
LGA    C    40_C      C    40_C     1.470     0    0.032   0.045     1.680   77.143   78.571
LGA    Q    41_C      Q    41_C     1.722     0    0.026   0.815     3.322   70.833   67.619
LGA    R    42_C      R    42_C     1.670     0    0.041   1.117     7.310   72.857   49.177
LGA    Y    43_C      Y    43_C     1.212     0    0.081   0.175     1.478   81.429   81.429
LGA    W    44_C      W    44_C     0.901     0    0.041   0.184     1.185   90.476   88.537
LGA    T    45_C      T    45_C     0.649     0    0.050   0.157     0.899   90.476   90.476
LGA    S    46_C      S    46_C     0.413     0    0.046   0.110     0.778   95.238   96.825
LGA    G    47_C      G    47_C     0.579     0    0.039   0.039     0.880   90.476   90.476
LGA    G    48_C      G    48_C     0.783     0    0.063   0.063     0.783   90.476   90.476
LGA    T    49_C      T    49_C     0.341     0    0.108   0.163     0.656   97.619   97.279
LGA    M    50_C      M    50_C     0.359     0    0.107   0.752     4.516   97.619   75.833
LGA    R    51_C      R    51_C     1.297     0    0.112   0.321     5.575   88.214   59.048
LGA    S    52_C      S    52_C     1.737     0    0.073   0.156     2.824   79.286   73.175
LGA    V    53_C      V    53_C     1.632     0    0.146   1.150     3.154   70.952   67.483
LGA    P    54_C      P    54_C     4.546     0    0.107   0.182     5.709   38.810   35.170
LGA    I    55_C      I    55_C     3.763     0    0.081   1.356     5.097   38.690   36.726
LGA    G    56_C      G    56_C     4.242     0    0.644   0.644     4.913   37.262   37.262

# 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):     2.106          2.103                  2.181           81.849   76.682

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     50    1.54    91.667    94.211     3.043

LGA_LOCAL      RMSD:   1.543  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.135  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.106  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.652595 * X  +  -0.264928 * Y  +  -0.709882 * Z  + -30.110460
  Y_new =   0.266301 * X  +   0.957307 * Y  +  -0.112457 * Z  +  -6.536424
  Z_new =   0.709368 * X  +  -0.115653 * Y  +   0.695285 * Z  +   6.897598 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.387439 -0.788601 -0.164830   [DEG:   22.1986  -45.1835   -9.4441 ]
ZXZ: -1.413685  0.801980  1.732411   [DEG:  -80.9982   45.9501   99.2598 ]
 
# END of job
