
#######################################################
#                                                     #
#                        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        2.29     2.29
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.57     2.32
  LCS_AVERAGE:     96.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.92     2.38
  LONGEST_CONTINUOUS_SEGMENT:    46       9_C - 54_C        0.98     2.41
  LCS_AVERAGE:     84.39

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    3   51      3    3    3    3    5    7    8    9   11   13   30   37   41   49   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C      4   50   51      3    4    9   17   23   34   40   47   47   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   50   51      3   14   39   44   46   47   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   50   51      6   38   43   45   46   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   50   51      5   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   50   51     27   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   50   51     27   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   50   51     20   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   50   51     31   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   50   51     29   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   50   51     33   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   50   51     20   39   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   50   51     14   38   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   50   51      4   38   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   50   51      4    5   36   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   50   51      4   34   43   45   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     46   50   51      3    5   16   37   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     13   50   51      3   11   29   43   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     13   50   51      3    3   23   37   47   48   49   49   49   50   50   50   50   50   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  93.54  (  84.39   96.23  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     33     39     43     45     47     48     49     49     49     50     50     50     50     50     51     51     51     51     51     51 
GDT PERCENT_AT  64.71  76.47  84.31  88.24  92.16  94.12  96.08  96.08  96.08  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    0.31   0.42   0.62   0.78   1.14   1.18   1.29   1.29   1.29   1.57   1.57   1.57   1.57   1.57   2.29   2.29   2.29   2.29   2.29   2.29
GDT RMS_ALL_AT   2.51   2.48   2.44   2.41   2.45   2.42   2.38   2.38   2.38   2.32   2.32   2.32   2.32   2.32   2.29   2.29   2.29   2.29   2.29   2.29

# 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    12.733     2    0.230   0.236    15.102    0.000    0.000
LGA    T     7_C      T     7_C     6.710     0    0.683   0.575     8.745   17.143   17.347
LGA    K     8_C      K     8_C     3.618     4    0.279   0.296     4.244   46.905   27.196
LGA    I     9_C      I     9_C     2.032     0    0.077   0.732     4.267   64.881   63.452
LGA    L    10_C      L    10_C     1.257     0    0.089   0.272     2.605   83.810   80.714
LGA    P    11_C      P    11_C     0.493     0    0.011   0.054     1.086   95.238   90.612
LGA    C    12_C      C    12_C     0.625     0    0.049   0.118     1.109   90.595   89.048
LGA    P    13_C      P    13_C     0.977     0    0.078   0.311     1.646   85.952   84.082
LGA    R    14_C      R    14_C     1.308     0    0.171   1.149     4.434   77.262   72.987
LGA    C    15_C      C    15_C     1.022     0    0.055   0.130     1.207   85.952   84.444
LGA    N    16_C      N    16_C     0.664     0    0.059   0.263     1.463   90.476   87.083
LGA    S    17_C      S    17_C     0.600     0    0.085   0.134     0.669   92.857   92.063
LGA    M    18_C      M    18_C     0.219     0    0.046   0.604     1.816   97.619   93.036
LGA    E    19_C      E    19_C     0.616     4    0.035   0.034     0.803   92.857   51.323
LGA    T    20_C      T    20_C     0.756     0    0.070   0.110     0.914   90.476   90.476
LGA    K    21_C      K    21_C     0.630     0    0.034   0.458     3.808   90.476   77.778
LGA    F    22_C      F    22_C     0.557     0    0.015   0.050     0.639   90.476   92.208
LGA    C    23_C      C    23_C     0.707     0    0.029   0.050     0.934   90.476   90.476
LGA    Y    24_C      Y    24_C     0.611     0    0.016   0.059     1.547   95.238   87.579
LGA    Y    25_C      Y    25_C     0.309     0    0.044   0.079     0.916  100.000   96.032
LGA    N    26_C      N    26_C     0.521     0    0.041   0.345     1.776   92.857   88.333
LGA    N    27_C      N    27_C     0.795     0    0.038   0.277     1.644   90.476   87.143
LGA    Y    28_C      Y    28_C     0.570     0    0.063   0.102     2.184   92.857   80.278
LGA    N    29_C      N    29_C     0.147     0    0.044   0.198     0.465  100.000  100.000
LGA    V    30_C      V    30_C     0.230     0    0.058   1.142     2.854  100.000   88.844
LGA    N    31_C      N    31_C     0.373     0    0.014   0.416     1.816  100.000   91.964
LGA    Q    32_C      Q    32_C     0.385     0    0.015   0.879     3.765   97.619   83.968
LGA    P    33_C      P    33_C     0.497     0    0.043   0.048     0.566   95.238   95.918
LGA    R    34_C      R    34_C     0.630     0    0.020   0.904     3.901   92.857   77.013
LGA    H    35_C      H    35_C     0.448     0    0.113   0.208     0.604   92.857   94.286
LGA    F    36_C      F    36_C     1.038     0    0.029   0.141     1.692   88.214   81.558
LGA    C    37_C      C    37_C     0.977     0    0.080   0.132     1.447   85.952   87.460
LGA    K    38_C      K    38_C     0.904     0    0.116   0.478     1.472   90.476   86.455
LGA    A    39_C      A    39_C     0.933     0    0.102   0.100     0.960   90.476   90.476
LGA    C    40_C      C    40_C     1.364     0    0.048   0.080     1.438   81.429   81.429
LGA    Q    41_C      Q    41_C     1.553     0    0.061   0.787     3.081   75.000   70.370
LGA    R    42_C      R    42_C     1.545     0    0.024   1.324     5.774   75.000   61.775
LGA    Y    43_C      Y    43_C     0.998     0    0.072   0.124     1.293   85.952   86.706
LGA    W    44_C      W    44_C     0.616     0    0.037   0.188     0.828   90.476   90.476
LGA    T    45_C      T    45_C     0.458     0    0.048   0.148     0.658   95.238   94.558
LGA    S    46_C      S    46_C     0.282     0    0.046   0.117     0.427  100.000  100.000
LGA    G    47_C      G    47_C     0.237     0    0.030   0.030     0.372  100.000  100.000
LGA    G    48_C      G    48_C     0.430     0    0.060   0.060     0.430  100.000  100.000
LGA    T    49_C      T    49_C     0.517     0    0.083   0.974     2.491   92.857   85.646
LGA    M    50_C      M    50_C     0.726     0    0.116   0.723     4.660   95.238   73.512
LGA    R    51_C      R    51_C     0.996     0    0.061   0.278     4.897   90.476   65.671
LGA    S    52_C      S    52_C     1.780     0    0.016   0.178     2.519   79.286   73.175
LGA    V    53_C      V    53_C     1.286     0    0.131   0.858     2.456   77.143   74.218
LGA    P    54_C      P    54_C     3.473     0    0.126   0.319     4.483   51.786   50.204
LGA    I    55_C      I    55_C     2.779     0    0.195   1.414     4.122   50.119   50.357
LGA    G    56_C      G    56_C     3.652     0    0.589   0.589     3.695   46.667   46.667

# 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):     2.285          2.269                  2.197           83.828   78.557

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     49    1.29    90.196    93.365     3.535

LGA_LOCAL      RMSD:   1.286  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.377  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.285  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.628124 * X  +   0.280101 * Y  +  -0.725950 * Z  + -28.240532
  Y_new =  -0.774829 * X  +   0.139519 * Y  +  -0.616583 * Z  +  -9.708405
  Z_new =  -0.071422 * X  +   0.949778 * Y  +   0.304665 * Z  +   8.188865 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.889588  0.071483  1.260390   [DEG:  -50.9697    4.0957   72.2150 ]
ZXZ: -0.866682  1.261209 -0.075057   [DEG:  -49.6572   72.2620   -4.3005 ]
 
# END of job
