
#######################################################
#                                                     #
#                        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   33 (  263),  selected   30 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   30 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      32_B - 61_B        1.16     1.16
  LCS_AVERAGE:     49.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      32_B - 61_B        1.16     1.16
  LCS_AVERAGE:     49.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      32_B - 60_B        0.92     1.20
  LCS_AVERAGE:     46.78

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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    32_B     L    32_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     M    33_B     M    33_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    34_B     K    34_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    35_B     K    35_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     L    36_B     L    36_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     F    37_B     F    37_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     D    38_B     D    38_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    39_B     A    39_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    40_B     A    40_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     H    41_B     H    41_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     R    42_B     R    42_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     N    43_B     N    43_B     29   30   30     12   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     D    44_B     D    44_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    45_B     K    45_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     D    46_B     D    46_B     29   30   30      8   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    47_B     K    47_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    48_B     V    48_B     29   30   30      8   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    49_B     K    49_B     29   30   30      8   20   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    50_B     K    50_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    51_B     V    51_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    52_B     V    52_B     29   30   30      8   19   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     E    53_B     E    53_B     29   30   30      6   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     E    54_B     E    54_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    55_B     A    55_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    56_B     K    56_B     29   30   30     10   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    57_B     K    57_B     29   30   30      6   23   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    58_B     V    58_B     29   30   30      4   14   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    59_B     V    59_B     29   30   30      4   22   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     S    60_B     S    60_B     29   30   30      3   13   28   29   29   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     T    61_B     T    61_B     15   30   30      3    5    9   21   25   30   30   30   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_AVERAGE  LCS_A:  48.38  (  46.78   49.18   49.18 )

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     23     28     29     29     30     30     30     30     30     30     30     30     30     30     30     30     30     30     30 
GDT PERCENT_AT  19.67  37.70  45.90  47.54  47.54  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18  49.18
GDT RMS_LOCAL    0.28   0.67   0.85   0.92   0.92   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16
GDT RMS_ALL_AT   2.61   1.39   1.26   1.20   1.20   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16   1.16

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    32_B      L    32_B     0.855     0    0.020   1.219     3.734   90.595   80.298
LGA    M    33_B      M    33_B     0.685     0    0.032   0.750     3.949   95.238   81.905
LGA    K    34_B      K    34_B     0.339     0    0.038   0.375     1.838   97.619   91.693
LGA    K    35_B      K    35_B     0.959     0    0.040   0.333     1.890   90.476   83.545
LGA    L    36_B      L    36_B     0.835     0    0.027   0.963     3.038   90.476   83.155
LGA    F    37_B      F    37_B     0.773     0    0.023   1.312     6.209   88.214   62.900
LGA    D    38_B      D    38_B     1.161     0    0.028   0.262     2.279   85.952   76.369
LGA    A    39_B      A    39_B     0.488     0    0.026   0.034     0.624   97.619   96.190
LGA    A    40_B      A    40_B     0.892     0    0.062   0.061     1.397   85.952   86.857
LGA    H    41_B      H    41_B     1.380     0    0.095   0.781     3.740   79.286   69.571
LGA    R    42_B      R    42_B     0.350     0    0.173   1.047     2.925   95.238   87.792
LGA    N    43_B      N    43_B     0.533     0    0.029   1.098     2.956   97.619   87.679
LGA    D    44_B      D    44_B     0.395     0    0.035   0.081     1.035  100.000   94.107
LGA    K    45_B      K    45_B     0.714     0    0.059   1.006     5.667   92.857   69.153
LGA    D    46_B      D    46_B     0.911     0    0.027   0.982     3.941   90.476   75.119
LGA    K    47_B      K    47_B     0.490     0    0.031   0.674     6.119   95.238   68.360
LGA    V    48_B      V    48_B     0.808     0    0.026   0.086     1.384   88.333   86.667
LGA    K    49_B      K    49_B     1.363     0    0.030   1.108     6.717   81.548   56.349
LGA    K    50_B      K    50_B     0.830     0    0.037   0.851     5.402   90.476   70.000
LGA    V    51_B      V    51_B     1.046     0    0.050   1.124     2.805   83.690   78.027
LGA    V    52_B      V    52_B     1.786     0    0.035   0.173     2.734   75.000   69.524
LGA    E    53_B      E    53_B     1.279     0    0.036   0.467     1.779   83.690   80.529
LGA    E    54_B      E    54_B     0.640     0    0.025   0.322     1.002   90.476   89.471
LGA    A    55_B      A    55_B     1.333     0    0.036   0.049     1.657   81.429   79.714
LGA    K    56_B      K    56_B     1.148     0    0.030   0.443     3.141   85.952   76.190
LGA    K    57_B      K    57_B     0.266     0    0.027   1.687     6.394   97.619   75.820
LGA    V    58_B      V    58_B     1.268     0    0.134   0.151     2.300   79.524   75.510
LGA    V    59_B      V    59_B     0.821     0    0.076   0.870     2.556   90.476   83.197
LGA    S    60_B      S    60_B     1.452     0    0.279   0.588     2.207   77.381   78.810
LGA    T    61_B      T    61_B     3.669     0    0.111   1.129     4.701   45.238   40.136

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     241    241  100.00                61
SUMMARY(RMSD_GDC):     1.162          1.153                  2.030           43.011   38.273

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   61    4.0     30    1.16    45.902    47.807     2.377

LGA_LOCAL      RMSD:   1.162  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.162  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:   1.162  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.999816 * X  +  -0.006498 * Y  +   0.018068 * Z  +  27.027506
  Y_new =  -0.017565 * X  +  -0.070561 * Y  +  -0.997353 * Z  + -30.201719
  Z_new =   0.007756 * X  +  -0.997486 * Y  +   0.070434 * Z  +  49.265911 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.124026 -0.007756 -1.500302   [DEG: -178.9935   -0.4444  -85.9610 ]
ZXZ:  0.018114  1.500304  3.133817   [DEG:    1.0379   85.9611  179.5545 ]
 
# END of job
