 
####################################################### 
#                                                     # 
#                        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: 133 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    43.29           63.3    30    14.0   214     ARMSMC  
     WELL ORDERED  . . . . .    30.58           64.3    28    15.5   181     ARMSMC  
     NO INTER CONTACTS . . .    43.32           65.5    29    17.7   164     ARMSMC  
     SHIFTED CHAIN . . . . .    61.25           45.5    11    10.0   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    21.94           78.9    19    23.8    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    28.78           50.0     2     4.3    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    52.01           62.5    16    12.1   132     ARMSMC  
     BURIED  . . . . . . . .    30.40           64.3    14    17.1    82     ARMSMC  
     CORE  . . . . . . . . .    44.14           64.3    28    16.7   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.90           46.7    15    16.0    94     ARMSSC1 
     WELL ORDERED  . . . . .    90.34           45.5    11    17.5    63     ARMSSC1 
     NO INTER CONTACTS . . .    85.76           42.9    14    18.7    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    78.50           53.8    13    15.9    82     ARMSSC1 
     CHANGED ANGLES  . . . .    62.41           50.0     4     8.5    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    34.22           80.0     5    10.6    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    96.74           33.3     9    25.0    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    75.64            0.0     1     4.8    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    70.22           57.1     7    12.1    58     ARMSSC1 
     BURIED  . . . . . . . .    92.58           37.5     8    22.2    36     ARMSSC1 
     CORE  . . . . . . . . .    83.40           50.0    14    19.2    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.25           63.6    11    18.0    61     ARMSSC2 
     WELL ORDERED  . . . . .    16.31          100.0     3     9.1    33     ARMSSC2 
     NO INTER CONTACTS . . .    72.25           63.6    11    21.6    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    68.64           62.5     8    19.0    42     ARMSSC2 
     CHANGED ANGLES  . . . .    89.68           42.9     7    17.5    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    34.15           75.0     4    14.8    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    86.87           57.1     7    25.9    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    66.65            0.0     1     7.7    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    72.76           57.1     7    18.4    38     ARMSSC2 
     BURIED  . . . . . . . .    71.37           75.0     4    17.4    23     ARMSSC2 
     CORE  . . . . . . . . .    72.79           70.0    10    20.8    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    53.30           50.0     4    22.2    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     NO INTER CONTACTS . . .    53.30           50.0     4    23.5    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    53.30           50.0     4    30.8    13     ARMSSC3 
     CHANGED ANGLES  . . . .    53.30           50.0     4    23.5    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    60.80           50.0     2    20.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    37.48           66.7     3    30.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    84.54            0.0     1    25.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    53.30           50.0     4    25.0    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .    37.48           66.7     3    21.4    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.37            0.0     1    16.7     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     NO INTER CONTACTS . . .    69.37            0.0     1    20.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .    69.37            0.0     1    16.7     6     ARMSSC4 
     CHANGED ANGLES  . . . .    69.37            0.0     1    25.0     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 . .    69.37            0.0     1    33.3     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 . . . . . . . .    69.37            0.0     1    16.7     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    69.37            0.0     1    16.7     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.16917     r(1,2) =  -0.72030     r(1,3) =   0.67272 
 r(2,1) =  -0.28102     r(2,2) =  -0.61897     r(2,3) =  -0.73341 
 r(3,1) =   0.94467     r(3,2) =  -0.31312     r(3,3) =  -0.09771 
THE OFFSET VECTOR: 
 v(1) =  64.89293     v(2) =  26.52980     v(3) =  36.66253 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.77           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.62         16    14.8   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2264                            CRMSCA  
     WELL ORDERED  . . . . .    3.74         15    16.5    91     CRMSCA  
     NO INTER CONTACTS . . .    3.20         15    18.1    83     CRMSCA  
     SHIFTED CHAIN . . . . .    3.33          6    10.7    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.95         10    25.0    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    1.31          1     4.2    24     CRMSCA  
     SURFACE . . . . . . . .    1.85          8    11.9    67     CRMSCA  
     BURIED  . . . . . . . .    4.78          8    19.5    41     CRMSCA  
     CORE  . . . . . . . . .    3.73         15    17.9    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.94         79    14.8   533     CRMSMC  
     WELL ORDERED  . . . . .    4.03         74    16.9   439     CRMSMC  
     NO INTER CONTACTS . . .    3.46         74    18.0   410     CRMSMC  
     SHIFTED CHAIN . . . . .    3.86         29    10.5   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    3.21         49    24.6   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    1.49          5     4.2   120     CRMSMC  
     SURFACE . . . . . . . .    2.26         39    11.7   332     CRMSMC  
     BURIED  . . . . . . . .    5.07         40    19.9   201     CRMSMC  
     CORE  . . . . . . . . .    4.05         74    17.9   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.58         69    17.0   405     CRMSSC  
     WELL ORDERED  . . . . .    4.53         42    15.3   274     CRMSSC  
     NO INTER CONTACTS . . .    4.57         66    20.2   327     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.32         57    17.6   323     CRMSSC  
     CHANGED ANGLES  . . . .    4.54         30    16.3   184     CRMSSC  
     SECONDARY STRUCTURE . .    3.95         47    26.7   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.14          5     6.0    83     CRMSSC  
     SURFACE . . . . . . . .    3.65         33    14.1   234     CRMSSC  
     BURIED  . . . . . . . .    5.29         36    21.1   171     CRMSSC  
     CORE  . . . . . . . . .    4.44         64    19.9   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    4.24        133    15.9   837     CRMSALL 
     WELL ORDERED  . . . . .    4.17        103    16.2   635     CRMSALL 
     NO INTER CONTACTS . . .    3.99        126    19.1   659     CRMSALL 
     SHIFTED CHAIN . . . . .    4.08         44    10.6   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    3.58         87    25.9   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.63          9     5.0   179     CRMSALL 
     SURFACE . . . . . . . .    3.02         65    12.9   502     CRMSALL 
     BURIED  . . . . . . . .    5.14         68    20.3   335     CRMSALL 
     CORE  . . . . . . . . .    4.21        124    18.8   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 . . . . . . . . . .    3.051      1.000       0.500     16    14.8   108     ERRCA  
     WELL ORDERED  . . . . .    3.206      1.000       0.500     15    16.5    91     ERRCA  
     NO INTER CONTACTS . . .    2.754      1.000       0.500     15    18.1    83     ERRCA  
     SHIFTED CHAIN . . . . .    2.364      1.000       0.500      6    10.7    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    2.776      1.000       0.500     10    25.0    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.312      1.000       0.500      1     4.2    24     ERRCA  
     SURFACE . . . . . . . .    1.704      1.000       0.500      8    11.9    67     ERRCA  
     BURIED  . . . . . . . .    4.399      1.000       0.500      8    19.5    41     ERRCA  
     CORE  . . . . . . . . .    3.167      1.000       0.500     15    17.9    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.305      1.000       0.500     79    14.8   533     ERRMC  
     WELL ORDERED  . . . . .    3.396      1.000       0.500     74    16.9   439     ERRMC  
     NO INTER CONTACTS . . .    2.984      1.000       0.500     74    18.0   410     ERRMC  
     SHIFTED CHAIN . . . . .    2.825      1.000       0.500     29    10.5   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    3.000      1.000       0.500     49    24.6   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.286      1.000       0.500      5     4.2   120     ERRMC  
     SURFACE . . . . . . . .    2.060      1.000       0.500     39    11.7   332     ERRMC  
     BURIED  . . . . . . . .    4.520      1.000       0.500     40    19.9   201     ERRMC  
     CORE  . . . . . . . . .    3.442      1.000       0.500     74    17.9   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.037      1.000       0.500     69    17.0   405     ERRSC  
     WELL ORDERED  . . . . .    3.968      1.000       0.500     42    15.3   274     ERRSC  
     NO INTER CONTACTS . . .    3.999      1.000       0.500     66    20.2   327     ERRSC  
     RELIABLE SIDE CHAINS  .    3.809      1.000       0.500     57    17.6   323     ERRSC  
     CHANGED ANGLES  . . . .    3.999      1.000       0.500     30    16.3   184     ERRSC  
     SHIFTED CHAIN . . . . .    3.750      1.000       0.500     20    10.4   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    3.554      1.000       0.500     47    26.7   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.799      1.000       0.500      5     6.0    83     ERRSC  
     SURFACE . . . . . . . .    3.227      1.000       0.500     33    14.1   234     ERRSC  
     BURIED  . . . . . . . .    4.780      1.000       0.500     36    21.1   171     ERRSC  
     CORE  . . . . . . . . .    3.900      1.000       0.500     64    19.9   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.628      1.000       0.500    133    15.9   837     ERRALL 
     WELL ORDERED  . . . . .    3.548      1.000       0.500    103    16.2   635     ERRALL 
     NO INTER CONTACTS . . .    3.439      1.000       0.500    126    19.1   659     ERRALL 
     SHIFTED CHAIN . . . . .    3.229      1.000       0.500     44    10.6   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    3.259      1.000       0.500     87    25.9   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.644      1.000       0.500      9     5.0   179     ERRALL 
     SURFACE . . . . . . . .    2.608      1.000       0.500     65    12.9   502     ERRALL 
     BURIED  . . . . . . . .    4.603      1.000       0.500     68    20.3   335     ERRALL 
     CORE  . . . . . . . . .    3.627      1.000       0.500    124    18.8   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         6         9        14        16      16     108   DISTCA 
CA  (P)      0.93      5.56      8.33     12.96     14.81             108   DISTCA 
CA  (RMS)    0.74      1.43      1.77      2.69      3.62                   DISTCA 
 
ALL (N)         3        34        66       103       131     133     837   DISTALL 
ALL (P)      0.36      4.06      7.89     12.31     15.65             837   DISTALL 
ALL (RMS)    0.64      1.51      2.06      2.85      4.06                   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            15             1          RMSLSI 
CA  (P)       77.78         13.89          0.93          RMSLSI 
CA  (RMS)      1.02          3.73          1.31          RMSLSI 
 
 
 
END of the results output 
