 
####################################################### 
#                                                     # 
#                        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: 124 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    90.60           46.4    28    13.1   214     ARMSMC  
     WELL ORDERED  . . . . .    98.25           36.4    22    12.2   181     ARMSMC  
     NO INTER CONTACTS . . .    92.18           43.5    23    14.0   164     ARMSMC  
     SHIFTED CHAIN . . . . .    94.05           41.7    24    21.8   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .   123.60            0.0     9    11.2    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    92.69           43.8    16    34.8    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    92.36           47.4    19    14.4   132     ARMSMC  
     BURIED  . . . . . . . .    86.76           44.4     9    11.0    82     ARMSMC  
     CORE  . . . . . . . . .    87.72           50.0    12     7.1   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.88           42.9    14    14.9    94     ARMSSC1 
     WELL ORDERED  . . . . .    81.39           50.0     8    12.7    63     ARMSSC1 
     NO INTER CONTACTS . . .    73.44           36.4    11    14.7    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    67.55           46.2    13    15.9    82     ARMSSC1 
     CHANGED ANGLES  . . . .    72.45           41.7    12    25.5    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    69.62           46.2    13    27.7    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    79.73           40.0     5    13.9    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    78.97           25.0     8    38.1    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    66.92           40.0    10    17.2    58     ARMSSC1 
     BURIED  . . . . . . . .    82.99           50.0     4    11.1    36     ARMSSC1 
     CORE  . . . . . . . . .    61.15           66.7     6     8.2    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.54           75.0     8    13.1    61     ARMSSC2 
     WELL ORDERED  . . . . .    61.48           80.0     5    15.2    33     ARMSSC2 
     NO INTER CONTACTS . . .    61.54           75.0     8    15.7    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    65.76           71.4     7    16.7    42     ARMSSC2 
     CHANGED ANGLES  . . . .    45.73           83.3     6    15.0    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    42.34           85.7     7    25.9    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    55.24           75.0     4    14.8    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    16.39          100.0     5    38.5    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    54.30           75.0     4    10.5    38     ARMSSC2 
     BURIED  . . . . . . . .    68.02           75.0     4    17.4    23     ARMSSC2 
     CORE  . . . . . . . . .    98.25           33.3     3     6.2    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   170.12            0.0     1     5.6    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     NO INTER CONTACTS . . .   170.12            0.0     1     5.9    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .   170.12            0.0     1     5.9    17     ARMSSC3 
     SHIFTED CHAIN . . . . .   170.12            0.0     1    10.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .   170.12            0.0     1    10.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .   170.12            0.0     1     6.2    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .   170.12            0.0     1     7.1    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) =   0.24457     r(1,2) =  -0.96895     r(1,3) =   0.03633 
 r(2,1) =   0.55738     r(2,2) =   0.10983     r(2,3) =  -0.82296 
 r(3,1) =   0.79342     r(3,2) =   0.22152     r(3,3) =   0.56694 
THE OFFSET VECTOR: 
 v(1) =  20.59851     v(2) =  12.34850     v(3) =  52.71253 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.64           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.89         15    13.9   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.5262                            CRMSCA  
     WELL ORDERED  . . . . .    8.74         12    13.2    91     CRMSCA  
     NO INTER CONTACTS . . .    8.15         12    14.5    83     CRMSCA  
     SHIFTED CHAIN . . . . .    8.36         13    23.2    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .   12.23          5    12.5    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.76          8    33.3    24     CRMSCA  
     SURFACE . . . . . . . .    6.79         10    14.9    67     CRMSCA  
     BURIED  . . . . . . . .    9.73          5    12.2    41     CRMSCA  
     CORE  . . . . . . . . .    9.78          7     8.3    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.05         74    13.9   533     CRMSMC  
     WELL ORDERED  . . . . .    8.86         56    12.8   439     CRMSMC  
     NO INTER CONTACTS . . .    8.40         59    14.4   410     CRMSMC  
     SHIFTED CHAIN . . . . .    8.45         65    23.6   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .   12.37         25    12.6   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.90         40    33.3   120     CRMSMC  
     SURFACE . . . . . . . .    7.00         50    15.1   332     CRMSMC  
     BURIED  . . . . . . . .    9.88         24    11.9   201     CRMSMC  
     CORE  . . . . . . . . .   10.01         34     8.2   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.94         64    15.8   405     CRMSSC  
     WELL ORDERED  . . . . .   14.34         46    16.8   274     CRMSSC  
     NO INTER CONTACTS . . .   13.39         56    17.1   327     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.29         58    18.0   323     CRMSSC  
     CHANGED ANGLES  . . . .   10.72         32    17.4   184     CRMSSC  
     SECONDARY STRUCTURE . .   17.00         32    18.2   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    9.55         31    37.3    83     CRMSSC  
     SURFACE . . . . . . . .    9.63         33    14.1   234     CRMSSC  
     BURIED  . . . . . . . .   15.71         31    18.1   171     CRMSSC  
     CORE  . . . . . . . . .   15.46         33    10.2   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.77        124    14.8   837     CRMSALL 
     WELL ORDERED  . . . . .   11.78         94    14.8   635     CRMSALL 
     NO INTER CONTACTS . . .   11.29        104    15.8   659     CRMSALL 
     SHIFTED CHAIN . . . . .   11.34        106    25.4   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .   15.32         52    15.5   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.85         63    35.2   179     CRMSALL 
     SURFACE . . . . . . . .    8.19         73    14.5   502     CRMSALL 
     BURIED  . . . . . . . .   13.63         51    15.2   335     CRMSALL 
     CORE  . . . . . . . . .   13.11         61     9.3   658     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.76      8   100.0     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     5.90     40   100.0    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     7.85     63   100.0    63      16-PSSPNFYS-23   
 ALL LOOP  2     0.00      0     0.0    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.06      8   100.0     8      16-PSSPNFYS-23   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.31     40   100.0    40      16-PSSPNFYS-23   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.84     63   100.0    63      16-PSSPNFYS-23   
 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 . . . . . . . . . .    5.902      1.000       0.500     15    13.9   108     ERRCA  
     WELL ORDERED  . . . . .    6.864      1.000       0.500     12    13.2    91     ERRCA  
     NO INTER CONTACTS . . .    6.190      1.000       0.500     12    14.5    83     ERRCA  
     SHIFTED CHAIN . . . . .    6.284      1.000       0.500     13    23.2    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .   11.586      1.000       0.500      5    12.5    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.522      1.000       0.500      8    33.3    24     ERRCA  
     SURFACE . . . . . . . .    5.099      1.000       0.500     10    14.9    67     ERRCA  
     BURIED  . . . . . . . .    7.508      1.000       0.500      5    12.2    41     ERRCA  
     CORE  . . . . . . . . .    7.479      1.000       0.500      7     8.3    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.138      1.000       0.500     74    13.9   533     ERRMC  
     WELL ORDERED  . . . . .    7.042      1.000       0.500     56    12.8   439     ERRMC  
     NO INTER CONTACTS . . .    6.496      1.000       0.500     59    14.4   410     ERRMC  
     SHIFTED CHAIN . . . . .    6.478      1.000       0.500     65    23.6   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .   11.693      1.000       0.500     25    12.6   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.760      1.000       0.500     40    33.3   120     ERRMC  
     SURFACE . . . . . . . .    5.406      1.000       0.500     50    15.1   332     ERRMC  
     BURIED  . . . . . . . .    7.662      1.000       0.500     24    11.9   201     ERRMC  
     CORE  . . . . . . . . .    7.759      1.000       0.500     34     8.2   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.918      1.000       0.500     64    15.8   405     ERRSC  
     WELL ORDERED  . . . . .   12.430      1.000       0.500     46    16.8   274     ERRSC  
     NO INTER CONTACTS . . .   11.386      1.000       0.500     56    17.1   327     ERRSC  
     RELIABLE SIDE CHAINS  .   11.262      1.000       0.500     58    18.0   323     ERRSC  
     CHANGED ANGLES  . . . .    9.643      1.000       0.500     32    17.4   184     ERRSC  
     SHIFTED CHAIN . . . . .   11.560      1.000       0.500     54    28.0   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .   16.045      1.000       0.500     32    18.2   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    8.318      1.000       0.500     31    37.3    83     ERRSC  
     SURFACE . . . . . . . .    8.368      1.000       0.500     33    14.1   234     ERRSC  
     BURIED  . . . . . . . .   13.632      1.000       0.500     31    18.1   171     ERRSC  
     CORE  . . . . . . . . .   13.360      1.000       0.500     33    10.2   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.481      1.000       0.500    124    14.8   837     ERRALL 
     WELL ORDERED  . . . . .    9.576      1.000       0.500     94    14.8   635     ERRALL 
     NO INTER CONTACTS . . .    9.026      1.000       0.500    104    15.8   659     ERRALL 
     SHIFTED CHAIN . . . . .    8.943      1.000       0.500    106    25.4   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .   14.291      1.000       0.500     52    15.5   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.411      1.000       0.500     63    35.2   179     ERRALL 
     SURFACE . . . . . . . .    6.608      1.000       0.500     73    14.5   502     ERRALL 
     BURIED  . . . . . . . .   11.163      1.000       0.500     51    15.2   335     ERRALL 
     CORE  . . . . . . . . .   10.619      1.000       0.500     61     9.3   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)         1         5         7         9        12      15     108   DISTCA 
CA  (P)      0.93      4.63      6.48      8.33     11.11             108   DISTCA 
CA  (RMS)    0.72      1.24      1.64      2.45      4.95                   DISTCA 
 
ALL (N)         6        23        31        50        81     124     837   DISTALL 
ALL (P)      0.72      2.75      3.70      5.97      9.68             837   DISTALL 
ALL (RMS)    0.73      1.33      1.62      2.71      5.42                   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             7             8          RMSLSI 
CA  (P)       77.78          6.48          7.41          RMSLSI 
CA  (RMS)      1.02          9.78          5.76          RMSLSI 
 
 
 
END of the results output 
