
#######################################################
#                                                     #
#                        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        2.22     2.22
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.38     2.25
  LCS_AVERAGE:     96.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48       8_C - 55_C        0.86     2.32
  LONGEST_CONTINUOUS_SEGMENT:    48       9_C - 56_C        0.89     2.36
  LCS_AVERAGE:     90.66

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    5   51      3    3    3    3    7    8    9   10   12   13   16   32   34   39   45   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C      3   50   51      3    3    5   12   14   27   38   48   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     48   50   51      3   11   33   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     48   50   51      9   40   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     48   50   51      9   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     48   50   51     30   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     48   50   51     30   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     48   50   51     28   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     48   50   51      9   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     48   50   51     28   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     48   50   51     27   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     48   50   51     30   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     48   50   51     10   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     48   50   51     31   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     48   50   51     14   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     48   50   51      4   21   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     48   50   51      4   36   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     48   50   51     21   42   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     48   50   51      3   16   42   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     48   50   51      3   28   46   47   48   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     48   50   51      3    4   10   21   47   48   49   49   50   50   50   50   50   50   50   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  95.66  (  90.66   96.31  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     31     42     46     47     48     48     49     49     50     50     50     50     50     50     50     51     51     51     51     51 
GDT PERCENT_AT  60.78  82.35  90.20  92.16  94.12  94.12  96.08  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
GDT RMS_LOCAL    0.34   0.50   0.66   0.72   0.86   0.86   1.00   1.00   1.38   1.38   1.38   1.38   1.38   1.38   1.38   2.22   2.22   2.22   2.22   2.22
GDT RMS_ALL_AT   2.41   2.38   2.35   2.36   2.32   2.32   2.32   2.32   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.22   2.22   2.22   2.22   2.22

# 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    13.203     2    0.196   0.199    15.625    0.000    0.000
LGA    T     7_C      T     7_C     7.055     0    0.682   0.536     9.205   17.262   15.238
LGA    K     8_C      K     8_C     3.277     4    0.349   0.367     4.278   50.357   29.577
LGA    I     9_C      I     9_C     1.515     0    0.060   0.749     2.849   75.119   75.238
LGA    L    10_C      L    10_C     1.167     0    0.077   0.250     2.475   85.952   80.536
LGA    P    11_C      P    11_C     0.193     0    0.014   0.055     0.643   97.619   95.918
LGA    C    12_C      C    12_C     0.361     0    0.047   0.126     0.650  100.000   98.413
LGA    P    13_C      P    13_C     0.433     0    0.115   0.329     1.205  100.000   95.986
LGA    R    14_C      R    14_C     0.889     0    0.180   1.009     2.704   88.214   84.199
LGA    C    15_C      C    15_C     1.017     0    0.055   0.159     1.235   85.952   87.460
LGA    N    16_C      N    16_C     0.747     0    0.044   0.264     0.767   90.476   94.048
LGA    S    17_C      S    17_C     0.656     0    0.087   0.135     0.695   90.476   90.476
LGA    M    18_C      M    18_C     0.672     0    0.046   0.795     2.848   90.476   84.107
LGA    E    19_C      E    19_C     0.595     4    0.056   0.055     0.636   90.476   50.265
LGA    T    20_C      T    20_C     0.646     0    0.070   0.078     0.921   92.857   91.837
LGA    K    21_C      K    21_C     0.325     0    0.030   0.473     2.795  100.000   90.265
LGA    F    22_C      F    22_C     0.395     0    0.015   0.045     0.476  100.000  100.000
LGA    C    23_C      C    23_C     0.422     0    0.076   0.083     0.557  100.000   98.413
LGA    Y    24_C      Y    24_C     0.349     0    0.019   0.104     1.465   97.619   91.389
LGA    Y    25_C      Y    25_C     0.312     0    0.043   0.089     0.732  100.000   96.032
LGA    N    26_C      N    26_C     0.373     0    0.051   0.252     1.227  100.000   94.167
LGA    N    27_C      N    27_C     0.468     0    0.027   0.205     1.399   97.619   92.917
LGA    Y    28_C      Y    28_C     0.370     0    0.073   0.098     1.635   97.619   87.619
LGA    N    29_C      N    29_C     0.308     0    0.050   0.190     0.878  100.000   98.810
LGA    V    30_C      V    30_C     0.307     0    0.053   1.141     2.656  100.000   88.844
LGA    N    31_C      N    31_C     0.376     0    0.015   0.411     1.420  100.000   95.298
LGA    Q    32_C      Q    32_C     0.299     0    0.017   0.906     4.512   97.619   79.206
LGA    P    33_C      P    33_C     0.613     0    0.031   0.043     0.704   90.476   90.476
LGA    R    34_C      R    34_C     0.670     0    0.023   1.020     3.119   95.238   82.078
LGA    H    35_C      H    35_C     0.490     0    0.082   0.184     0.717   97.619   94.286
LGA    F    36_C      F    36_C     0.607     0    0.024   0.123     0.875   90.476   90.476
LGA    C    37_C      C    37_C     0.519     0    0.081   0.139     0.781   92.857   92.063
LGA    K    38_C      K    38_C     0.557     0    0.110   0.489     1.454   95.238   90.582
LGA    A    39_C      A    39_C     0.758     0    0.103   0.102     0.996   90.476   90.476
LGA    C    40_C      C    40_C     0.745     0    0.046   0.060     0.779   90.476   90.476
LGA    Q    41_C      Q    41_C     0.721     0    0.015   0.773     2.968   90.476   81.111
LGA    R    42_C      R    42_C     0.632     0    0.026   1.143     3.025   90.476   82.814
LGA    Y    43_C      Y    43_C     0.437     0    0.076   0.105     1.022   97.619   92.103
LGA    W    44_C      W    44_C     0.484     0    0.056   0.152     0.723   97.619   96.599
LGA    T    45_C      T    45_C     0.504     0    0.060   0.127     0.880   92.857   91.837
LGA    S    46_C      S    46_C     0.383     0    0.059   0.148     0.759   95.238   96.825
LGA    G    47_C      G    47_C     0.835     0    0.057   0.057     1.065   88.214   88.214
LGA    G    48_C      G    48_C     0.448     0    0.055   0.055     0.538   97.619   97.619
LGA    T    49_C      T    49_C     0.219     0    0.106   0.158     0.663  100.000   98.639
LGA    M    50_C      M    50_C     0.758     0    0.097   0.750     4.048   92.857   75.893
LGA    R    51_C      R    51_C     1.307     0    0.093   0.338     4.002   88.214   65.065
LGA    S    52_C      S    52_C     1.129     0    0.046   0.179     1.503   83.690   80.079
LGA    V    53_C      V    53_C     0.569     0    0.146   1.140     3.025   90.476   81.293
LGA    P    54_C      P    54_C     1.887     0    0.140   0.342     3.168   77.143   70.884
LGA    I    55_C      I    55_C     1.535     0    0.094   1.347     2.955   69.048   71.131
LGA    G    56_C      G    56_C     3.652     0    0.673   0.673     4.385   43.690   43.690

# 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):     2.216          2.196                  2.054           87.918   82.764

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     49    1.00    92.647    94.743     4.441

LGA_LOCAL      RMSD:   1.003  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.315  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.216  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.847391 * X  +  -0.486945 * Y  +  -0.211690 * Z  + -29.248400
  Y_new =  -0.254130 * X  +  -0.722004 * Y  +   0.643528 * Z  +  -7.357196
  Z_new =  -0.466204 * X  +  -0.491524 * Y  +  -0.735567 * Z  +   5.417402 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.291362  0.484995 -2.552513   [DEG:  -16.6938   27.7882 -146.2482 ]
ZXZ: -2.823791  2.397299 -2.382626   [DEG: -161.7913  137.3551 -136.5144 ]
 
# END of job
