
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A     34   34   34      4   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     34   34   34      3   12   30   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     34   34   34      3   12   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     34   34   34     11   16   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     34   34   34     15   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     34   34   34     15   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     34   34   34     11   17   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  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     17     30     32     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  50.00  88.24  94.12 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.58   0.69   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_AT   1.05   0.90   0.91   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

# Checking swapping
#   possible swapping detected:  D    20_B      D    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     0.579     0    0.115   0.703     2.427   92.857   87.778
LGA    G     2_B      G     2_A     0.878     0    0.066   0.066     0.878   90.476   90.476
LGA    P     3_B      P     3_A     0.294     0    0.211   0.198     1.487   90.595   89.320
LGA    N     4_B      N     4_A     0.840     0    0.688   1.179     5.422   82.143   68.155
LGA    G     5_B      G     5_A     2.241     0    0.675   0.675     2.845   66.905   66.905
LGA    G     6_B      G     6_A     1.749     0    0.062   0.062     2.340   72.976   72.976
LGA    V     7_B      V     7_A     0.477     0    0.134   0.185     0.756   97.619   94.558
LGA    C     8_B      C     8_A     0.539     0    0.013   0.047     0.589   95.238   95.238
LGA    P     9_B      P     9_A     0.609     0    0.046   0.279     1.478   92.857   90.544
LGA    V    10_B      V    10_A     0.832     0    0.332   0.985     3.140   88.214   79.728
LGA    L    11_B      L    11_A     1.754     3    0.098   0.129     1.858   75.000   46.607
LGA    I    12_B      I    12_A     0.578     0    0.017   0.647     2.467   95.238   88.512
LGA    Y    13_B      Y    13_A     0.572     0    0.029   0.346     3.535   95.238   74.762
LGA    L    14_B      L    14_A     0.801     0    0.031   1.377     3.847   90.476   76.250
LGA    C    15_B      C    15_A     0.596     0    0.019   0.038     0.668   90.476   93.651
LGA    R    16_B      R    16_A     0.401     0    0.102   1.474     8.553   97.619   54.935
LGA    R    17_B      R    17_A     0.535     0    0.028   1.002     4.595   95.238   79.957
LGA    D    18_B      D    18_A     0.753     0    0.019   0.051     0.898   90.476   90.476
LGA    S    19_B      S    19_A     1.060     0    0.015   0.080     1.244   85.952   85.952
LGA    D    20_B      D    20_A     0.777     0    0.060   0.136     1.069   88.214   91.726
LGA    C    21_B      C    21_A     0.251     0    0.020   0.071     0.475  100.000  100.000
LGA    P    22_B      P    22_A     0.614     0    0.061   0.159     0.916   92.857   91.837
LGA    G    23_B      G    23_A     0.433     0    0.045   0.045     0.495  100.000  100.000
LGA    E    24_B      E    24_A     0.505     0    0.041   0.233     1.434   97.619   92.646
LGA    C    25_B      C    25_A     0.314     0    0.022   0.041     0.690   95.238   96.825
LGA    I    26_B      I    26_A     0.720     0    0.056   0.081     1.257   90.476   88.214
LGA    C    27_B      C    27_A     0.488     0    0.022   0.053     0.644   92.857   95.238
LGA    L    28_B      L    28_A     0.721     0    0.029   0.099     1.678   92.857   86.071
LGA    G    29_B      G    29_A     0.802     0    0.027   0.027     1.267   85.952   85.952
LGA    N    30_B      N    30_A     1.548     0    0.050   0.122     2.099   79.286   76.131
LGA    G    31_B      G    31_A     0.758     0    0.076   0.076     0.851   90.476   90.476
LGA    Y    32_B      Y    32_A     0.187     0    0.029   0.131     0.850  100.000   95.238
LGA    C    33_B      C    33_A     0.334     0    0.030   0.047     0.372  100.000  100.000
LGA    G    34_B      G    34_A     0.529     0    0.303   0.303     1.271   92.976   92.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     0.863          0.890                  1.549           90.718   85.591

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    0.86    97.059    98.633     3.530

LGA_LOCAL      RMSD:   0.863  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.863  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   0.863  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.334903 * X  +   0.766870 * Y  +   0.547494 * Z  + -36.045879
  Y_new =   0.560643 * X  +  -0.629180 * Y  +   0.538342 * Z  + -30.911343
  Z_new =   0.757311 * X  +   0.126657 * Y  +  -0.640655 * Z  + -23.251307 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.032324 -0.859186  2.946410   [DEG:   59.1478  -49.2277  168.8169 ]
ZXZ:  2.347765  2.266147  1.405084   [DEG:  134.5170  129.8406   80.5054 ]
 
# END of job
