 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_1.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_1.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_1.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_1.5icb.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1087 atoms, MODEL 846 atoms, 310 common with TARGET 
           Number of atoms possible to evaluate: 256 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 2.655663 
 
 CA-RMS TARGET<->PARENT(1ncx)	 2.782501 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.224615 
 
 CA-RMS TARGET<->PARENT(5icb)	 2.843657 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.69           68.9   122    87.1   140     ARMSMC  
     WELL ORDERED  . . . . .    52.69           68.9   122    87.1   140     ARMSMC  
     NO INTER CONTACTS . . .    52.69           68.9   122    87.1   140     ARMSMC  
     SHIFTED CHAIN . . . . .    55.02           67.3   110    85.9   128     ARMSMC  
     ALTERNATIVE PARENT  . .    42.26           85.7    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    12.62           96.9    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    74.24           48.5    33    68.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    54.37           67.4    92    83.6   110     ARMSMC  
     BURIED  . . . . . . . .    47.17           73.3    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    41.99           76.4    89    96.7    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     1     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.02080     r(1,2) =  -0.84419     r(1,3) =  -0.53563 
 r(2,1) =  -0.79187     r(2,2) =   0.34097     r(2,3) =  -0.50664 
 r(3,1) =   0.61034     r(3,2) =   0.41361     r(3,3) =  -0.67558 
THE OFFSET VECTOR: 
 v(1) =  20.35869     v(2) =  19.10143     v(3) = -36.04525 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.79           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   16.79         64    90.1    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2624                            CRMSCA  
     WELL ORDERED  . . . . .   16.79         64    90.1    71     CRMSCA  
     NO INTER CONTACTS . . .   16.79         64    90.1    71     CRMSCA  
     SHIFTED CHAIN . . . . .   17.37         58    89.2    65     CRMSCA  
     ALTERNATIVE PARENT  . .   13.55          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .   14.82         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .   15.04         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.30         19    76.0    25     CRMSCA  
     SURFACE . . . . . . . .   17.21         49    87.5    56     CRMSCA  
     BURIED  . . . . . . . .   15.35         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .   18.36         45    97.8    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   16.62        256    73.1   350     CRMSMC  
     WELL ORDERED  . . . . .   16.62        256    73.1   350     CRMSMC  
     NO INTER CONTACTS . . .   16.62        256    73.1   350     CRMSMC  
     SHIFTED CHAIN . . . . .   17.18        232    72.3   321     CRMSMC  
     ALTERNATIVE PARENT  . .   13.06         32    82.1    39     CRMSMC  
     SECONDARY STRUCTURE . .   14.52        128    80.5   159     CRMSMC  
     SHIFTED SS UNITS  . . .   14.78         64    80.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.04         76    61.8   123     CRMSMC  
     SURFACE . . . . . . . .   16.99        196    71.0   276     CRMSMC  
     BURIED  . . . . . . . .   15.36         60    81.1    74     CRMSMC  
     CORE  . . . . . . . . .   18.21        180    79.3   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   803     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   803     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   767     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   156     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   234     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   624     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   179     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   16.62        256    23.6  1087     CRMSALL 
     WELL ORDERED  . . . . .   16.62        256    23.6  1087     CRMSALL 
     NO INTER CONTACTS . . .   16.62        256    23.6  1087     CRMSALL 
     SHIFTED CHAIN . . . . .   17.18        232    23.1  1003     CRMSALL 
     ALTERNATIVE PARENT  . .   13.06         32    29.4   109     CRMSALL 
     SECONDARY STRUCTURE . .   14.52        128    24.5   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.04         76    22.8   334     CRMSALL 
     SURFACE . . . . . . . .   16.99        196    23.1   848     CRMSALL 
     BURIED  . . . . . . . .   15.36         60    25.1   239     CRMSALL 
     CORE  . . . . . . . . .   18.21        180    23.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     8.62      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     7.07      9    75.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    24.10      3    50.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     8.23     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     6.54     36    61.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    23.72     12    41.4    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     8.23     20    32.3    62       1-STDDS-5    
 ALL LOOP  2     6.54     36    22.0   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    23.72     12    14.3    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.95      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     4.20      9    75.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     0.11      3    50.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.07     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     4.20     36    61.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     0.93     12    41.4    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.07     20    32.3    62       1-STDDS-5    
 ALL LOOP  2     4.20     36    22.0   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     0.93     12    14.3    84      66-PNGFDM-71   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.503      1.000       0.500     64    90.1    71     ERRCA  
     WELL ORDERED  . . . . .   14.503      1.000       0.500     64    90.1    71     ERRCA  
     NO INTER CONTACTS . . .   14.503      1.000       0.500     64    90.1    71     ERRCA  
     SHIFTED CHAIN . . . . .   15.215      1.000       0.500     58    89.2    65     ERRCA  
     ALTERNATIVE PARENT  . .   11.427      1.000       0.500      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .   12.888      1.000       0.500     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.318      1.000       0.500     19    76.0    25     ERRCA  
     SURFACE . . . . . . . .   14.775      1.000       0.500     49    87.5    56     ERRCA  
     BURIED  . . . . . . . .   13.613      1.000       0.500     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .   16.269      1.000       0.500     45    97.8    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.326      1.000       0.500    256    73.1   350     ERRMC  
     WELL ORDERED  . . . . .   14.326      1.000       0.500    256    73.1   350     ERRMC  
     NO INTER CONTACTS . . .   14.326      1.000       0.500    256    73.1   350     ERRMC  
     SHIFTED CHAIN . . . . .   14.978      1.000       0.500    232    72.3   321     ERRMC  
     ALTERNATIVE PARENT  . .   10.977      1.000       0.500     32    82.1    39     ERRMC  
     SECONDARY STRUCTURE . .   12.605      1.000       0.500    128    80.5   159     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.042      1.000       0.500     76    61.8   123     ERRMC  
     SURFACE . . . . . . . .   14.547      1.000       0.500    196    71.0   276     ERRMC  
     BURIED  . . . . . . . .   13.603      1.000       0.500     60    81.1    74     ERRMC  
     CORE  . . . . . . . . .   16.134      1.000       0.500    180    79.3   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   803     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   803     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   803     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   767     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   743     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    77     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   234     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   624     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   179     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.326      1.000       0.500    256    23.6  1087     ERRALL 
     WELL ORDERED  . . . . .   14.326      1.000       0.500    256    23.6  1087     ERRALL 
     NO INTER CONTACTS . . .   14.326      1.000       0.500    256    23.6  1087     ERRALL 
     SHIFTED CHAIN . . . . .   14.978      1.000       0.500    232    23.1  1003     ERRALL 
     ALTERNATIVE PARENT  . .   10.977      1.000       0.500     32    29.4   109     ERRALL 
     SECONDARY STRUCTURE . .   12.605      1.000       0.500    128    24.5   522     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.042      1.000       0.500     76    22.8   334     ERRALL 
     SURFACE . . . . . . . .   14.547      1.000       0.500    196    23.1   848     ERRALL 
     BURIED  . . . . . . . .   13.603      1.000       0.500     60    25.1   239     ERRALL 
     CORE  . . . . . . . . .   16.134      1.000       0.500    180    23.9   753     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         1         5         7         8        26      64      71   DISTCA 
CA  (P)      1.41      7.04      9.86     11.27     36.62              71   DISTCA 
CA  (RMS)    0.87      1.59      1.79      2.43      6.70                   DISTCA 
 
ALL (N)         2        10        16        40       108     256    1087   DISTALL 
ALL (P)      0.18      0.92      1.47      3.68      9.94            1087   DISTALL 
ALL (RMS)    0.79      1.50      1.93      3.22      6.47                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          46            45            19          RMSLSI 
CA  (P)       64.79         63.38         26.76          RMSLSI 
CA  (RMS)      1.65         18.36         12.30          RMSLSI 
 
 
 
END of the results output 
