
#######################################################
#                                                     #
#                        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:    36       9_C - 44_C        4.93     6.82
  LCS_AVERAGE:     62.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       6_C - 19_C        1.89    11.27
  LCS_AVERAGE:     16.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       9_C - 19_C        0.92     9.67
  LCS_AVERAGE:     11.88

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      5   14   33      0    4    7    9   12   17   20   22   22   23   26   27   27   35   38   41   43   46   47   48 
LCS_GDT     T     7_C     T     7_C      5   14   33      3    4    7    8   12   17   20   22   22   23   26   27   33   36   39   44   45   46   47   48 
LCS_GDT     K     8_C     K     8_C      6   14   34      3    4    7   12   15   18   20   22   22   25   31   33   36   40   42   44   45   46   47   48 
LCS_GDT     I     9_C     I     9_C     11   14   36      3    7   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     L    10_C     L    10_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     P    11_C     P    11_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     C    12_C     C    12_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     P    13_C     P    13_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     R    14_C     R    14_C     11   14   36      7   10   11   13   15   18   20   22   22   28   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     C    15_C     C    15_C     11   14   36      5   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     N    16_C     N    16_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     S    17_C     S    17_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     M    18_C     M    18_C     11   14   36      7   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     E    19_C     E    19_C     11   14   36      4    9   11   12   13   17   19   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     T    20_C     T    20_C      9   13   36      4    6   10   12   12   13   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     K    21_C     K    21_C      8   13   36      3    6    9   12   12   13   15   17   22   25   31   34   38   40   42   44   45   46   47   48 
LCS_GDT     F    22_C     F    22_C      8   13   36      3    4    9   12   12   13   15   17   22   25   31   34   38   40   42   44   45   46   47   48 
LCS_GDT     C    23_C     C    23_C      5    7   36      3    4    6    6    7   10   14   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     Y    24_C     Y    24_C      5    7   36      3    4    6    6    7    9   13   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     Y    25_C     Y    25_C      5    7   36      3    4    6    6    7    9   12   20   22   27   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     N    26_C     N    26_C      5    7   36      3    4    6    6    7   10   14   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     N    27_C     N    27_C      5    7   36      3    4    6    6    7    9   14   20   22   27   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     Y    28_C     Y    28_C      3    6   36      3    3    3    5    7   12   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     N    29_C     N    29_C      3    6   36      3    4    5    8   10   12   15   18   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     V    30_C     V    30_C      3    6   36      3    3    3    7   10   11   15   18   22   28   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     N    31_C     N    31_C      4    6   36      3    4    5    8   10   12   15   18   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     Q    32_C     Q    32_C      4    6   36      3    4    6    8   10   12   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     P    33_C     P    33_C      4    6   36      3    4    5    5    7   10   12   16   20   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     R    34_C     R    34_C      5    8   36      4    5    5    7    9   13   20   22   22   23   31   32   36   40   42   44   45   46   47   48 
LCS_GDT     H    35_C     H    35_C      5    8   36      4    5    5    7   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     F    36_C     F    36_C      5    8   36      3    5    5    7    9   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     C    37_C     C    37_C      5    8   36      5   10   11   13   15   18   20   22   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     K    38_C     K    38_C      5    8   36      5    5   11   13   15   18   20   22   22   24   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     A    39_C     A    39_C      5    8   36      5    5    7    8   10   18   20   22   22   23   23   28   33   40   42   44   45   46   47   48 
LCS_GDT     C    40_C     C    40_C      5    8   36      5    5   11   13   15   18   20   22   22   23   23   29   33   37   42   44   45   46   47   48 
LCS_GDT     Q    41_C     Q    41_C      5    8   36      5    5    9   13   15   18   20   22   22   23   23   26   32   36   40   42   45   46   47   48 
LCS_GDT     R    42_C     R    42_C      3    4   36      3    3    3    3    5    7    8   18   22   24   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     Y    43_C     Y    43_C      3    4   36      1    3    3    6    6    9   12   18   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     W    44_C     W    44_C      3    3   36      3    3    4    6    6    9   13   18   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     T    45_C     T    45_C      4    5   20      4    4    5    6    6    9   12   18   20   23   29   34   37   39   42   44   45   46   47   48 
LCS_GDT     S    46_C     S    46_C      4    5   20      4    4    5    6    6    6    8   11   13   14   17   18   19   21   23   26   29   32   39   43 
LCS_GDT     G    47_C     G    47_C      4    5   20      4    4    5    6    6    6    8    9    9   10   15   17   19   22   24   27   33   35   39   43 
LCS_GDT     G    48_C     G    48_C      4    5   20      4    4    5    6    6    9   12   14   17   20   28   34   37   39   42   44   45   46   47   48 
LCS_GDT     T    49_C     T    49_C      3    5   20      3    3    4    5    7   10   13   18   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     M    50_C     M    50_C      4    5   20      3    5    6    8   10   12   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     R    51_C     R    51_C      4    5   20      3    4    4    4    5   10   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     S    52_C     S    52_C      5    5   20      3    4    5    8   10   12   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     V    53_C     V    53_C      5    5   20      3    4    5    8   10   12   15   20   22   29   33   35   38   40   42   44   45   46   47   48 
LCS_GDT     P    54_C     P    54_C      5    5   20      3    4    5    6    6   12   14   18   22   25   31   34   38   40   42   43   45   46   47   48 
LCS_GDT     I    55_C     I    55_C      5    5   20      3    4    5    6    7   10   12   15   21   25   29   34   37   39   41   43   45   46   47   48 
LCS_GDT     G    56_C     G    56_C      5    5   15      3    4    5    5    6    7    8   12   13   14   17   22   28   31   33   33   40   42   42   43 
LCS_AVERAGE  LCS_A:  30.51  (  11.88   16.96   62.71 )

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      7     10     11     13     15     18     20     22     22     29     33     35     38     40     42     44     45     46     47     48 
GDT PERCENT_AT  13.73  19.61  21.57  25.49  29.41  35.29  39.22  43.14  43.14  56.86  64.71  68.63  74.51  78.43  82.35  86.27  88.24  90.20  92.16  94.12
GDT RMS_LOCAL    0.32   0.51   0.77   1.10   1.45   1.92   2.25   2.43   2.43   3.85   4.06   4.23   4.49   4.69   4.93   5.17   5.26   5.37   5.49   5.64
GDT RMS_ALL_AT   9.11   9.26   9.21  10.59  10.55  10.78  10.82  10.80  10.80   6.66   6.65   6.64   6.63   6.63   6.62   6.62   6.58   6.57   6.58   6.59

# Checking swapping
#   possible swapping detected:  F    36_C      F    36_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     3.005     2    0.557   0.590     4.615   45.357   31.224
LGA    T     7_C      T     7_C     3.515     0    0.675   1.382     6.463   43.690   43.129
LGA    K     8_C      K     8_C     1.667     4    0.145   0.182     2.012   72.976   40.529
LGA    I     9_C      I     9_C     0.981     0    0.043   0.713     4.683   85.952   77.500
LGA    L    10_C      L    10_C     2.717     0    0.052   0.126     5.519   64.881   49.821
LGA    P    11_C      P    11_C     2.399     0    0.088   0.399     2.990   60.952   59.320
LGA    C    12_C      C    12_C     1.988     0    0.044   0.136     2.225   68.810   71.587
LGA    P    13_C      P    13_C     3.009     0    0.068   0.169     3.741   55.357   53.129
LGA    R    14_C      R    14_C     1.674     0    0.058   2.085     7.219   68.810   56.926
LGA    C    15_C      C    15_C     2.172     0    0.600   0.799     4.815   56.548   58.016
LGA    N    16_C      N    16_C     2.571     0    0.159   0.738     6.229   62.857   47.679
LGA    S    17_C      S    17_C     1.380     0    0.098   0.182     2.049   77.143   75.794
LGA    M    18_C      M    18_C     1.203     0    0.179   0.863     2.752   81.429   77.321
LGA    E    19_C      E    19_C     3.523     4    0.485   0.442     5.569   41.667   22.646
LGA    T    20_C      T    20_C     6.130     0    0.106   1.184     7.531   20.833   16.803
LGA    K    21_C      K    21_C     9.917     0    0.589   1.042    14.014    0.833    0.370
LGA    F    22_C      F    22_C    11.600     0    0.031   1.230    19.710    0.000    0.000
LGA    C    23_C      C    23_C     8.920     0    0.593   0.632     9.659    1.071    3.095
LGA    Y    24_C      Y    24_C    11.084     0    0.098   1.316    14.235    0.000    0.000
LGA    Y    25_C      Y    25_C    10.876     0    0.187   0.182    12.421    0.000    0.317
LGA    N    26_C      N    26_C    11.225     0    0.088   1.059    12.041    0.000    0.000
LGA    N    27_C      N    27_C    13.904     0    0.390   1.320    18.453    0.000    0.000
LGA    Y    28_C      Y    28_C    18.389     0    0.681   1.242    20.975    0.000    0.000
LGA    N    29_C      N    29_C    20.157     0    0.162   1.345    23.706    0.000    0.000
LGA    V    30_C      V    30_C    19.048     0    0.557   0.979    22.141    0.000    0.000
LGA    N    31_C      N    31_C    17.412     0    0.611   1.320    23.111    0.000    0.000
LGA    Q    32_C      Q    32_C     9.991     0    0.144   1.171    12.597    2.619   10.265
LGA    P    33_C      P    33_C     9.211     0    0.259   0.340    12.526    8.095    4.626
LGA    R    34_C      R    34_C     3.406     0    0.271   1.107     8.875   35.238   25.844
LGA    H    35_C      H    35_C     2.137     0    0.053   1.012     7.493   62.857   42.905
LGA    F    36_C      F    36_C     3.045     0    0.098   1.306     8.528   59.167   31.818
LGA    C    37_C      C    37_C     1.832     0    0.295   0.610     2.861   75.238   70.476
LGA    K    38_C      K    38_C     2.259     0    0.135   1.107    10.101   60.952   36.825
LGA    A    39_C      A    39_C     3.302     0    0.106   0.123     3.942   53.571   51.524
LGA    C    40_C      C    40_C     1.473     0    0.212   0.807     1.656   75.000   77.143
LGA    Q    41_C      Q    41_C     1.503     0    0.405   1.414     4.495   72.976   58.201
LGA    R    42_C      R    42_C     6.441     0    0.590   1.305    14.049   14.881    6.104
LGA    Y    43_C      Y    43_C    10.802     0    0.582   1.274    18.099    0.714    0.238
LGA    W    44_C      W    44_C    11.071     0    0.581   1.259    16.752    0.000    0.068
LGA    T    45_C      T    45_C    16.017     0    0.589   1.050    19.050    0.000    0.000
LGA    S    46_C      S    46_C    22.022     0    0.118   0.625    24.962    0.000    0.000
LGA    G    47_C      G    47_C    24.237     0    0.175   0.175    24.237    0.000    0.000
LGA    G    48_C      G    48_C    18.747     0    0.589   0.589    20.302    0.000    0.000
LGA    T    49_C      T    49_C    15.188     0    0.141   1.079    18.819    0.000    0.000
LGA    M    50_C      M    50_C    10.170     0    0.112   0.861    11.946    0.000    0.714
LGA    R    51_C      R    51_C    11.280     0    0.153   1.326    23.809    0.000    0.000
LGA    S    52_C      S    52_C    10.761     0    0.577   0.866    12.891    0.000    0.079
LGA    V    53_C      V    53_C    12.991     0    0.201   1.226    16.428    0.119    0.068
LGA    P    54_C      P    54_C    12.085     0    0.170   0.344    15.268    0.000    0.000
LGA    I    55_C      I    55_C    11.440     0    0.179   0.801    14.432    0.000    0.417
LGA    G    56_C      G    56_C    18.192     0    0.079   0.079    20.276    0.000    0.000

# 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):     6.538          6.561                  7.458           28.051   23.579

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     22    2.43    43.627    37.357     0.868

LGA_LOCAL      RMSD:   2.434  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.802  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.538  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.217832 * X  +  -0.455004 * Y  +   0.863435 * Z  + -56.552525
  Y_new =  -0.700105 * X  +  -0.543538 * Y  +  -0.463055 * Z  +  13.304822
  Z_new =   0.680002 * X  +  -0.705363 * Y  +  -0.200151 * Z  +  10.009493 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.872444 -0.747765 -1.847284   [DEG: -107.2831  -42.8438 -105.8416 ]
ZXZ:  1.078537  1.772308  2.374499   [DEG:   61.7956  101.5458  136.0488 ]
 
# END of job
