 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0009.inter 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0009.2cbp.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 837 atoms, MODEL 975 atoms, 828 common with TARGET 
           Number of atoms possible to evaluate: 140 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    95.75           34.4    32    15.0   214     ARMSMC  
     WELL ORDERED  . . . . .    87.95           30.8    26    14.4   181     ARMSMC  
     NO INTER CONTACTS . . .   100.71           34.6    26    15.9   164     ARMSMC  
     SHIFTED CHAIN . . . . .   103.92           38.5    13    11.8   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    95.42           45.5    11    13.8    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    85.51           60.0     5    10.9    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.49           41.2    17    12.9   132     ARMSMC  
     BURIED  . . . . . . . .   101.37           26.7    15    18.3    82     ARMSMC  
     CORE  . . . . . . . . .    97.52           29.6    27    16.1   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.49           33.3    15    16.0    94     ARMSSC1 
     WELL ORDERED  . . . . .    97.01           33.3    12    19.0    63     ARMSSC1 
     NO INTER CONTACTS . . .   100.76           30.8    13    17.3    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .   101.87           28.6    14    17.1    82     ARMSSC1 
     CHANGED ANGLES  . . . .   110.47           50.0     4     8.5    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    98.92           60.0     5    10.6    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    72.58           33.3     6    16.7    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   155.25            0.0     2     9.5    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .   116.69           28.6     7    12.1    58     ARMSSC1 
     BURIED  . . . . . . . .    79.21           37.5     8    22.2    36     ARMSSC1 
     CORE  . . . . . . . . .    86.51           38.5    13    17.8    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.46           46.2    13    21.3    61     ARMSSC2 
     WELL ORDERED  . . . . .    71.56           66.7     9    27.3    33     ARMSSC2 
     NO INTER CONTACTS . . .    77.91           45.5    11    21.6    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    59.82           57.1     7    16.7    42     ARMSSC2 
     CHANGED ANGLES  . . . .    86.31           33.3     6    15.0    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.44           50.0     4    14.8    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    49.33           66.7     6    22.2    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS   102.63            0.0     1     7.7    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    83.97           33.3     6    15.8    38     ARMSSC2 
     BURIED  . . . . . . . .    83.03           57.1     7    30.4    23     ARMSSC2 
     CORE  . . . . . . . . .    81.66           50.0    12    25.0    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    62.53           25.0     4    22.2    18     ARMSSC3 
     WELL ORDERED  . . . . .   110.56            0.0     1    33.3     3     ARMSSC3 
     NO INTER CONTACTS . . .    62.53           25.0     4    23.5    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    33.76           33.3     3    23.1    13     ARMSSC3 
     CHANGED ANGLES  . . . .    62.53           25.0     4    23.5    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    40.12            0.0     1    10.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    68.39           33.3     3    30.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    40.12            0.0     1    25.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    72.16            0.0     3    18.8    16     ARMSSC3 
     BURIED  . . . . . . . .     4.77          100.0     1    50.0     2     ARMSSC3 
     CORE  . . . . . . . . .    68.39           33.3     3    21.4    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     1     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     3     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) =   0.57099     r(1,2) =   0.73917     r(1,3) =  -0.35722 
 r(2,1) =  -0.14256     r(2,2) =   0.51779     r(2,3) =   0.84355 
 r(3,1) =   0.80849     r(3,2) =  -0.43073     r(3,3) =   0.40103 
THE OFFSET VECTOR: 
 v(1) =  52.43526     v(2) =  40.99161     v(3) =  59.21221 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.34           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   18.09         17    15.7   108     CRMSCA  
     CRN = ALL/NP  . . . . .    1.0641                            CRMSCA  
     WELL ORDERED  . . . . .   17.49         14    15.4    91     CRMSCA  
     NO INTER CONTACTS . . .   19.30         14    16.9    83     CRMSCA  
     SHIFTED CHAIN . . . . .   22.14          7    12.5    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .   18.27          6    15.0    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   29.92          3    12.5    24     CRMSCA  
     SURFACE . . . . . . . .   19.66          9    13.4    67     CRMSCA  
     BURIED  . . . . . . . .   16.14          8    19.5    41     CRMSCA  
     CORE  . . . . . . . . .   14.34         14    16.7    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   18.35         85    15.9   533     CRMSMC  
     WELL ORDERED  . . . . .   17.26         69    15.7   439     CRMSMC  
     NO INTER CONTACTS . . .   19.57         70    17.1   410     CRMSMC  
     SHIFTED CHAIN . . . . .   22.34         35    12.7   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .   18.61         30    15.1   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   29.96         15    12.5   120     CRMSMC  
     SURFACE . . . . . . . .   19.86         45    13.6   332     CRMSMC  
     BURIED  . . . . . . . .   16.48         40    19.9   201     CRMSMC  
     CORE  . . . . . . . . .   14.71         70    16.9   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   19.22         72    17.8   405     CRMSSC  
     WELL ORDERED  . . . . .   16.45         56    20.4   274     CRMSSC  
     NO INTER CONTACTS . . .   19.95         62    19.0   327     CRMSSC  
     RELIABLE SIDE CHAINS  .   19.86         52    16.1   323     CRMSSC  
     CHANGED ANGLES  . . . .   25.83         24    13.0   184     CRMSSC  
     SECONDARY STRUCTURE . .   18.62         31    17.6   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS   36.39          9    10.8    83     CRMSSC  
     SURFACE . . . . . . . .   22.05         31    13.2   234     CRMSSC  
     BURIED  . . . . . . . .   16.76         41    24.0   171     CRMSSC  
     CORE  . . . . . . . . .   15.26         63    19.6   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   18.79        140    16.7   837     CRMSALL 
     WELL ORDERED  . . . . .   16.81        111    17.5   635     CRMSALL 
     NO INTER CONTACTS . . .   19.77        118    17.9   659     CRMSALL 
     SHIFTED CHAIN . . . . .   24.63         51    12.2   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .   18.67         55    16.4   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS   32.72         21    11.7   179     CRMSALL 
     SURFACE . . . . . . . .   20.86         67    13.3   502     CRMSALL 
     BURIED  . . . . . . . .   16.66         73    21.8   335     CRMSALL 
     CORE  . . . . . . . . .   15.05        119    18.1   658     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     8      16-PSSPNFYS-23   
 CA  LOOP  2     0.00      0     0.0     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    40      16-PSSPNFYS-23   
 MC  LOOP  2     0.00      0     0.0    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    63      16-PSSPNFYS-23   
 ALL LOOP  2     0.00      0     0.0    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.119      1.000       0.500     17    15.7   108     ERRCA  
     WELL ORDERED  . . . . .   12.796      1.000       0.500     14    15.4    91     ERRCA  
     NO INTER CONTACTS . . .   13.953      1.000       0.500     14    16.9    83     ERRCA  
     SHIFTED CHAIN . . . . .   16.973      1.000       0.500      7    12.5    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .   13.267      1.000       0.500      6    15.0    40     ERRCA  
     LARGE SHIFTS/INSERTIONS   25.330      1.000       0.500      3    12.5    24     ERRCA  
     SURFACE . . . . . . . .   13.613      1.000       0.500      9    13.4    67     ERRCA  
     BURIED  . . . . . . . .   12.563      1.000       0.500      8    19.5    41     ERRCA  
     CORE  . . . . . . . . .   10.502      1.000       0.500     14    16.7    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.426      1.000       0.500     85    15.9   533     ERRMC  
     WELL ORDERED  . . . . .   12.740      1.000       0.500     69    15.7   439     ERRMC  
     NO INTER CONTACTS . . .   14.252      1.000       0.500     70    17.1   410     ERRMC  
     SHIFTED CHAIN . . . . .   17.342      1.000       0.500     35    12.7   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .   13.623      1.000       0.500     30    15.1   199     ERRMC  
     LARGE SHIFTS/INSERTIONS   25.297      1.000       0.500     15    12.5   120     ERRMC  
     SURFACE . . . . . . . .   13.892      1.000       0.500     45    13.6   332     ERRMC  
     BURIED  . . . . . . . .   12.902      1.000       0.500     40    19.9   201     ERRMC  
     CORE  . . . . . . . . .   10.882      1.000       0.500     70    16.9   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.818      1.000       0.500     72    17.8   405     ERRSC  
     WELL ORDERED  . . . . .   12.616      1.000       0.500     56    20.4   274     ERRSC  
     NO INTER CONTACTS . . .   15.248      1.000       0.500     62    19.0   327     ERRSC  
     RELIABLE SIDE CHAINS  .   14.977      1.000       0.500     52    16.1   323     ERRSC  
     CHANGED ANGLES  . . . .   21.971      1.000       0.500     24    13.0   184     ERRSC  
     SHIFTED CHAIN . . . . .   22.709      1.000       0.500     23    11.9   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .   14.791      1.000       0.500     31    17.6   176     ERRSC  
     LARGE SHIFTS/INSERTIONS   34.683      1.000       0.500      9    10.8    83     ERRSC  
     SURFACE . . . . . . . .   16.192      1.000       0.500     31    13.2   234     ERRSC  
     BURIED  . . . . . . . .   13.780      1.000       0.500     41    24.0   171     ERRSC  
     CORE  . . . . . . . . .   11.980      1.000       0.500     63    19.6   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.105      1.000       0.500    140    16.7   837     ERRALL 
     WELL ORDERED  . . . . .   12.595      1.000       0.500    111    17.5   635     ERRALL 
     NO INTER CONTACTS . . .   14.741      1.000       0.500    118    17.9   659     ERRALL 
     SHIFTED CHAIN . . . . .   19.695      1.000       0.500     51    12.2   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .   14.265      1.000       0.500     55    16.4   336     ERRALL 
     LARGE SHIFTS/INSERTIONS   29.147      1.000       0.500     21    11.7   179     ERRALL 
     SURFACE . . . . . . . .   14.898      1.000       0.500     67    13.3   502     ERRALL 
     BURIED  . . . . . . . .   13.378      1.000       0.500     73    21.8   335     ERRALL 
     CORE  . . . . . . . . .   11.451      1.000       0.500    119    18.1   658     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)         3         5         7         7         8      17     108   DISTCA 
CA  (P)      2.78      4.63      6.48      6.48      7.41             108   DISTCA 
CA  (RMS)    0.59      1.01      1.65      1.65      2.57                   DISTCA 
 
ALL (N)        13        24        33        55        68     140     837   DISTALL 
ALL (P)      1.55      2.87      3.94      6.57      8.12             837   DISTALL 
ALL (RMS)    0.63      1.08      1.61      2.75      3.92                   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)          84            14             3          RMSLSI 
CA  (P)       77.78         12.96          2.78          RMSLSI 
CA  (RMS)      1.02         14.34         29.92          RMSLSI 
 
 
 
END of the results output 
