 
####################################################### 
#                                                     # 
#                        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: 121 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   109.33           25.0    28    13.1   214     ARMSMC  
     WELL ORDERED  . . . . .   113.28           30.8    13     7.2   181     ARMSMC  
     NO INTER CONTACTS . . .   118.78           14.3    14     8.5   164     ARMSMC  
     SHIFTED CHAIN . . . . .   109.12           15.0    20    18.2   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .   118.79           40.0     5     6.2    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS   109.72           18.8    16    34.8    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .   106.76           26.1    23    17.4   132     ARMSMC  
     BURIED  . . . . . . . .   120.47           20.0     5     6.1    82     ARMSMC  
     CORE  . . . . . . . . .   108.82           33.3    12     7.1   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.96           28.6    14    14.9    94     ARMSSC1 
     WELL ORDERED  . . . . .    81.65           50.0     4     6.3    63     ARMSSC1 
     NO INTER CONTACTS . . .    73.42           37.5     8    10.7    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    77.72           33.3    12    14.6    82     ARMSSC1 
     CHANGED ANGLES  . . . .    63.58           30.0    10    21.3    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.09           18.2    11    23.4    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .   109.52            0.0     2     5.6    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    71.08           12.5     8    38.1    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    74.45           27.3    11    19.0    58     ARMSSC1 
     BURIED  . . . . . . . .    72.15           33.3     3     8.3    36     ARMSSC1 
     CORE  . . . . . . . . .    77.63           50.0     6     8.2    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.26           40.0    10    16.4    61     ARMSSC2 
     WELL ORDERED  . . . . .    73.96           33.3     3     9.1    33     ARMSSC2 
     NO INTER CONTACTS . . .    30.58           66.7     6    11.8    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    33.19           57.1     7    16.7    42     ARMSSC2 
     CHANGED ANGLES  . . . .    79.11           25.0     8    20.0    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    67.53           37.5     8    29.6    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    21.16          100.0     2     7.4    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    79.77           40.0     5    38.5    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    74.78           33.3     9    23.7    38     ARMSSC2 
     BURIED  . . . . . . . .    21.25          100.0     1     4.3    23     ARMSSC2 
     CORE  . . . . . . . . .    61.58           40.0     5    10.4    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    14.80          100.0     2    11.1    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     NO INTER CONTACTS . . .    14.80          100.0     2    11.8    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    14.80          100.0     2    15.4    13     ARMSSC3 
     CHANGED ANGLES  . . . .    14.80          100.0     2    11.8    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    14.80          100.0     2    20.0    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    15.63          100.0     1    25.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    14.80          100.0     2    12.5    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .    13.92          100.0     1     7.1    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    12.20          100.0     1    16.7     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     NO INTER CONTACTS . . .    12.20          100.0     1    20.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .    12.20          100.0     1    16.7     6     ARMSSC4 
     CHANGED ANGLES  . . . .    12.20          100.0     1    25.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .    12.20          100.0     1    33.3     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 . . . . . . . .    12.20          100.0     1    16.7     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    12.20          100.0     1    16.7     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.87554     r(1,2) =   0.45620     r(1,3) =  -0.15911 
 r(2,1) =   0.26342     r(2,2) =   0.17466     r(2,3) =  -0.94874 
 r(3,1) =  -0.40502     r(3,2) =  -0.87257     r(3,3) =  -0.27309 
THE OFFSET VECTOR: 
 v(1) = -19.71947     v(2) =  61.74246     v(3) = 103.88657 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.36           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.39         15    13.9   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.9594                            CRMSCA  
     WELL ORDERED  . . . . .   20.42          7     7.7    91     CRMSCA  
     NO INTER CONTACTS . . .   16.75          8     9.6    83     CRMSCA  
     SHIFTED CHAIN . . . . .   10.13         11    19.6    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .   26.91          3     7.5    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.21          8    33.3    24     CRMSCA  
     SURFACE . . . . . . . .   12.43         12    17.9    67     CRMSCA  
     BURIED  . . . . . . . .   20.44          3     7.3    41     CRMSCA  
     CORE  . . . . . . . . .   20.78          7     8.3    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.32         75    14.1   533     CRMSMC  
     WELL ORDERED  . . . . .   20.45         34     7.7   439     CRMSMC  
     NO INTER CONTACTS . . .   16.72         40     9.8   410     CRMSMC  
     SHIFTED CHAIN . . . . .   10.28         55    19.9   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .   26.65         15     7.5   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.62         40    33.3   120     CRMSMC  
     SURFACE . . . . . . . .   12.42         60    18.1   332     CRMSMC  
     BURIED  . . . . . . . .   20.20         15     7.5   201     CRMSMC  
     CORE  . . . . . . . . .   20.60         35     8.5   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   15.42         61    15.1   405     CRMSSC  
     WELL ORDERED  . . . . .   21.15         23     8.4   274     CRMSSC  
     NO INTER CONTACTS . . .   18.13         36    11.0   327     CRMSSC  
     RELIABLE SIDE CHAINS  .   16.70         51    15.8   323     CRMSSC  
     CHANGED ANGLES  . . . .   11.13         36    19.6   184     CRMSSC  
     SECONDARY STRUCTURE . .   28.32         12     6.8   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.79         29    34.9    83     CRMSSC  
     SURFACE . . . . . . . .   12.38         50    21.4   234     CRMSSC  
     BURIED  . . . . . . . .   24.95         11     6.4   171     CRMSSC  
     CORE  . . . . . . . . .   20.57         32     9.9   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.87        121    14.5   837     CRMSALL 
     WELL ORDERED  . . . . .   20.59         51     8.0   635     CRMSALL 
     NO INTER CONTACTS . . .   17.43         68    10.3   659     CRMSALL 
     SHIFTED CHAIN . . . . .   12.07         94    22.5   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .   27.51         24     7.1   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.75         61    34.1   179     CRMSALL 
     SURFACE . . . . . . . .   12.40         98    19.5   502     CRMSALL 
     BURIED  . . . . . . . .   22.54         23     6.9   335     CRMSALL 
     CORE  . . . . . . . . .   20.57         60     9.1   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     3.21      8   100.0     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     3.62     40   100.0    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     4.75     61   100.0    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     2.63      8   100.0     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     3.07     40   100.0    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     4.08     61   100.0    61      63-VNSDNDVE-70   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.391      1.000       0.500     15    13.9   108     ERRCA  
     WELL ORDERED  . . . . .   18.482      1.000       0.500      7     7.7    91     ERRCA  
     NO INTER CONTACTS . . .   12.541      1.000       0.500      8     9.6    83     ERRCA  
     SHIFTED CHAIN . . . . .    6.323      1.000       0.500     11    19.6    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .   26.800      1.000       0.500      3     7.5    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.440      1.000       0.500      8    33.3    24     ERRCA  
     SURFACE . . . . . . . .    8.768      1.000       0.500     12    17.9    67     ERRCA  
     BURIED  . . . . . . . .   16.885      1.000       0.500      3     7.3    41     ERRCA  
     CORE  . . . . . . . . .   19.479      1.000       0.500      7     8.3    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.491      1.000       0.500     75    14.1   533     ERRMC  
     WELL ORDERED  . . . . .   18.584      1.000       0.500     34     7.7   439     ERRMC  
     NO INTER CONTACTS . . .   12.826      1.000       0.500     40     9.8   410     ERRMC  
     SHIFTED CHAIN . . . . .    6.606      1.000       0.500     55    19.9   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .   26.522      1.000       0.500     15     7.5   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.778      1.000       0.500     40    33.3   120     ERRMC  
     SURFACE . . . . . . . .    8.952      1.000       0.500     60    18.1   332     ERRMC  
     BURIED  . . . . . . . .   16.647      1.000       0.500     15     7.5   201     ERRMC  
     CORE  . . . . . . . . .   19.305      1.000       0.500     35     8.5   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.027      1.000       0.500     61    15.1   405     ERRSC  
     WELL ORDERED  . . . . .   19.713      1.000       0.500     23     8.4   274     ERRSC  
     NO INTER CONTACTS . . .   14.542      1.000       0.500     36    11.0   327     ERRSC  
     RELIABLE SIDE CHAINS  .   13.436      1.000       0.500     51    15.8   323     ERRSC  
     CHANGED ANGLES  . . . .    8.778      1.000       0.500     36    19.6   184     ERRSC  
     SHIFTED CHAIN . . . . .   10.151      1.000       0.500     50    25.9   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .   28.240      1.000       0.500     12     6.8   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.452      1.000       0.500     29    34.9    83     ERRSC  
     SURFACE . . . . . . . .    9.636      1.000       0.500     50    21.4   234     ERRSC  
     BURIED  . . . . . . . .   22.893      1.000       0.500     11     6.4   171     ERRSC  
     CORE  . . . . . . . . .   18.891      1.000       0.500     32     9.9   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.245      1.000       0.500    121    14.5   837     ERRALL 
     WELL ORDERED  . . . . .   18.829      1.000       0.500     51     8.0   635     ERRALL 
     NO INTER CONTACTS . . .   13.684      1.000       0.500     68    10.3   659     ERRALL 
     SHIFTED CHAIN . . . . .    8.468      1.000       0.500     94    22.5   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .   27.411      1.000       0.500     24     7.1   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.551      1.000       0.500     61    34.1   179     ERRALL 
     SURFACE . . . . . . . .    9.301      1.000       0.500     98    19.5   502     ERRALL 
     BURIED  . . . . . . . .   19.528      1.000       0.500     23     6.9   335     ERRALL 
     CORE  . . . . . . . . .   19.068      1.000       0.500     60     9.1   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)         0         6         6         7         8      15     108   DISTCA 
CA  (P)      0.00      5.56      5.56      6.48      7.41             108   DISTCA 
CA  (RMS)    0.00      1.36      1.36      1.98      3.21                   DISTCA 
 
ALL (N)         4        23        36        50        67     121     837   DISTALL 
ALL (P)      0.48      2.75      4.30      5.97      8.00             837   DISTALL 
ALL (RMS)    0.82      1.37      1.77      2.55      4.89                   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         20.78          3.21          RMSLSI 
 
 
 
END of the results output 
