 
####################################################### 
#                                                     # 
#                        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: 113 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.29           41.4    29    13.6   214     ARMSMC  
     WELL ORDERED  . . . . .    74.29           41.4    29    16.0   181     ARMSMC  
     NO INTER CONTACTS . . .    71.38           42.9    21    12.8   164     ARMSMC  
     SHIFTED CHAIN . . . . .    61.24           63.6    11    10.0   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    35.29           33.3     6     7.5    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    59.94           66.7     3     6.5    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    79.35           33.3    18    13.6   132     ARMSMC  
     BURIED  . . . . . . . .    65.16           54.5    11    13.4    82     ARMSMC  
     CORE  . . . . . . . . .    75.77           38.5    26    15.5   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    76.79           53.8    13    13.8    94     ARMSSC1 
     WELL ORDERED  . . . . .    76.79           53.8    13    20.6    63     ARMSSC1 
     NO INTER CONTACTS . . .    80.12           44.4     9    12.0    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    65.51           60.0    10    12.2    82     ARMSSC1 
     CHANGED ANGLES  . . . .    68.85           62.5     8    17.0    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    63.68           66.7     6    12.8    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .   116.36            0.0     3     8.3    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    52.46           50.0     2     9.5    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    76.77           55.6     9    15.5    58     ARMSSC1 
     BURIED  . . . . . . . .    76.82           50.0     4    11.1    36     ARMSSC1 
     CORE  . . . . . . . . .    80.42           54.5    11    15.1    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    99.46           33.3     6     9.8    61     ARMSSC2 
     WELL ORDERED  . . . . .    85.77           40.0     5    15.2    33     ARMSSC2 
     NO INTER CONTACTS . . .    85.77           40.0     5     9.8    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    95.85           25.0     4     9.5    42     ARMSSC2 
     CHANGED ANGLES  . . . .    91.22           40.0     5    12.5    40     ARMSSC2 
     SHIFTED CHAIN . . . . .     2.83          100.0     1     3.7    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    95.04           50.0     2     7.4    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     2.83          100.0     1     7.7    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .   117.70            0.0     3     7.9    38     ARMSSC2 
     BURIED  . . . . . . . .    77.03           66.7     3    13.0    23     ARMSSC2 
     CORE  . . . . . . . . .   108.95           20.0     5    10.4    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     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    17     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    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 . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     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     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) =   0.39584     r(1,2) =   0.75609     r(1,3) =   0.52119 
 r(2,1) =   0.64459     r(2,2) =   0.17547     r(2,3) =  -0.74412 
 r(3,1) =  -0.65407     r(3,2) =   0.63051     r(3,3) =  -0.41791 
THE OFFSET VECTOR: 
 v(1) =  41.28503     v(2) =  21.41128     v(3) =  63.69130 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.60           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   10.89         16    14.8   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.6809                            CRMSCA  
     WELL ORDERED  . . . . .   11.16         15    16.5    91     CRMSCA  
     NO INTER CONTACTS . . .    9.10         12    14.5    83     CRMSCA  
     SHIFTED CHAIN . . . . .   15.32          7    12.5    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.32          3     7.5    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   15.69          3    12.5    24     CRMSCA  
     SURFACE . . . . . . . .    9.75         10    14.9    67     CRMSCA  
     BURIED  . . . . . . . .   12.58          6    14.6    41     CRMSCA  
     CORE  . . . . . . . . .    9.45         13    15.5    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   11.49         76    14.3   533     CRMSMC  
     WELL ORDERED  . . . . .   11.69         73    16.6   439     CRMSMC  
     NO INTER CONTACTS . . .    9.71         56    13.7   410     CRMSMC  
     SHIFTED CHAIN . . . . .   16.15         33    12.0   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.72         15     7.5   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.32         13    10.8   120     CRMSMC  
     SURFACE . . . . . . . .   10.13         48    14.5   332     CRMSMC  
     BURIED  . . . . . . . .   13.49         28    13.9   201     CRMSMC  
     CORE  . . . . . . . . .    9.86         63    15.3   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.17         50    12.3   405     CRMSSC  
     WELL ORDERED  . . . . .   13.42         48    17.5   274     CRMSSC  
     NO INTER CONTACTS . . .   12.26         38    11.6   327     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.45         38    11.8   323     CRMSSC  
     CHANGED ANGLES  . . . .   13.57         22    12.0   184     CRMSSC  
     SECONDARY STRUCTURE . .    6.57         13     7.4   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS   21.85          5     6.0    83     CRMSSC  
     SURFACE . . . . . . . .   10.77         28    12.0   234     CRMSSC  
     BURIED  . . . . . . . .   15.70         22    12.9   171     CRMSSC  
     CORE  . . . . . . . . .   11.82         45    14.0   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   12.13        113    13.5   837     CRMSALL 
     WELL ORDERED  . . . . .   12.38        108    17.0   635     CRMSALL 
     NO INTER CONTACTS . . .   10.81         85    12.9   659     CRMSALL 
     SHIFTED CHAIN . . . . .   16.79         43    10.3   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    5.01         25     7.4   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS   18.53         16     8.9   179     CRMSALL 
     SURFACE . . . . . . . .   10.30         67    13.3   502     CRMSALL 
     BURIED  . . . . . . . .   14.38         46    13.7   335     CRMSALL 
     CORE  . . . . . . . . .   10.72         97    14.7   658     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    26.50      1    12.5     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    27.59      5    12.5    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    27.67      7    11.1    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 . . . . . . . . . .    7.329      1.000       0.500     16    14.8   108     ERRCA  
     WELL ORDERED  . . . . .    7.441      1.000       0.500     15    16.5    91     ERRCA  
     NO INTER CONTACTS . . .    5.541      1.000       0.500     12    14.5    83     ERRCA  
     SHIFTED CHAIN . . . . .   12.102      1.000       0.500      7    12.5    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.744      1.000       0.500      3     7.5    40     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.392      1.000       0.500      3    12.5    24     ERRCA  
     SURFACE . . . . . . . .    6.375      1.000       0.500     10    14.9    67     ERRCA  
     BURIED  . . . . . . . .    8.918      1.000       0.500      6    14.6    41     ERRCA  
     CORE  . . . . . . . . .    6.391      1.000       0.500     13    15.5    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.885      1.000       0.500     76    14.3   533     ERRMC  
     WELL ORDERED  . . . . .    8.072      1.000       0.500     73    16.6   439     ERRMC  
     NO INTER CONTACTS . . .    5.977      1.000       0.500     56    13.7   410     ERRMC  
     SHIFTED CHAIN . . . . .   12.743      1.000       0.500     33    12.0   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    2.333      1.000       0.500     15     7.5   199     ERRMC  
     LARGE SHIFTS/INSERTIONS   12.472      1.000       0.500     13    10.8   120     ERRMC  
     SURFACE . . . . . . . .    6.833      1.000       0.500     48    14.5   332     ERRMC  
     BURIED  . . . . . . . .    9.687      1.000       0.500     28    13.9   201     ERRMC  
     CORE  . . . . . . . . .    6.938      1.000       0.500     63    15.3   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.630      1.000       0.500     50    12.3   405     ERRSC  
     WELL ORDERED  . . . . .   10.926      1.000       0.500     48    17.5   274     ERRSC  
     NO INTER CONTACTS . . .    9.729      1.000       0.500     38    11.6   327     ERRSC  
     RELIABLE SIDE CHAINS  .   10.968      1.000       0.500     38    11.8   323     ERRSC  
     CHANGED ANGLES  . . . .   10.787      1.000       0.500     22    12.0   184     ERRSC  
     SHIFTED CHAIN . . . . .   15.801      1.000       0.500     16     8.3   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    5.841      1.000       0.500     13     7.4   176     ERRSC  
     LARGE SHIFTS/INSERTIONS   18.876      1.000       0.500      5     6.0    83     ERRSC  
     SURFACE . . . . . . . .    8.082      1.000       0.500     28    12.0   234     ERRSC  
     BURIED  . . . . . . . .   13.873      1.000       0.500     22    12.9   171     ERRSC  
     CORE  . . . . . . . . .    9.714      1.000       0.500     45    14.0   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.943      1.000       0.500    113    13.5   837     ERRALL 
     WELL ORDERED  . . . . .    9.200      1.000       0.500    108    17.0   635     ERRALL 
     NO INTER CONTACTS . . .    7.527      1.000       0.500     85    12.9   659     ERRALL 
     SHIFTED CHAIN . . . . .   13.609      1.000       0.500     43    10.3   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    4.057      1.000       0.500     25     7.4   336     ERRALL 
     LARGE SHIFTS/INSERTIONS   14.022      1.000       0.500     16     8.9   179     ERRALL 
     SURFACE . . . . . . . .    7.228      1.000       0.500     67    13.3   502     ERRALL 
     BURIED  . . . . . . . .   11.442      1.000       0.500     46    13.7   335     ERRALL 
     CORE  . . . . . . . . .    8.106      1.000       0.500     97    14.7   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         6         8         9        12      16     108   DISTCA 
CA  (P)      2.78      5.56      7.41      8.33     11.11             108   DISTCA 
CA  (RMS)    0.74      1.38      1.60      1.99      4.13                   DISTCA 
 
ALL (N)         6        23        33        55        73     113     837   DISTALL 
ALL (P)      0.72      2.75      3.94      6.57      8.72             837   DISTALL 
ALL (RMS)    0.75      1.34      1.79      2.79      4.37                   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            13             3          RMSLSI 
CA  (P)       77.78         12.04          2.78          RMSLSI 
CA  (RMS)      1.02          9.45         15.69          RMSLSI 
 
 
 
END of the results output 
