 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0004.1csp.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0004.1mjc.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 588 atoms, MODEL 461 atoms, 421 common with TARGET 
           Number of atoms possible to evaluate: 289 
 
 
 CA-RMS TARGET<->PARENT(1csp)	 2.141282 
 
 CA-RMS TARGET<->PARENT(1mjc)	 2.434782 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    94.10           26.5   102    68.0   150     ARMSMC  
     WELL ORDERED  . . . . .    94.10           26.5   102    68.0   150     ARMSMC  
     NO INTER CONTACTS . . .    94.10           26.5   102    68.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    94.85           24.2    91    65.9   138     ARMSMC  
     ALTERNATIVE PARENT  . .    77.45           66.7     6    60.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    93.15           33.3    36    66.7    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    85.59           30.0    40    64.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    96.34           26.0    73    68.9   106     ARMSMC  
     BURIED  . . . . . . . .    88.18           27.6    29    65.9    44     ARMSMC  
     CORE  . . . . . . . . .    99.20           24.2    62    70.5    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    46     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    12     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) =  -0.32973     r(1,2) =  -0.68059     r(1,3) =  -0.65428 
 r(2,1) =   0.42612     r(2,2) =  -0.72571     r(2,3) =   0.54015 
 r(3,1) =  -0.84244     r(3,2) =  -0.10070     r(3,3) =   0.52930 
THE OFFSET VECTOR: 
 v(1) =  20.77085     v(2) =   6.96479     v(3) =   2.99365 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.97           (Number of atoms:    5) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.80         59    77.6    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2508                            CRMSCA  
     WELL ORDERED  . . . . .   14.80         59    77.6    76     CRMSCA  
     NO INTER CONTACTS . . .   14.80         59    77.6    76     CRMSCA  
     SHIFTED CHAIN . . . . .   15.04         53    75.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .   16.10          3    60.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   13.00         21    77.8    27     CRMSCA  
     SHIFTED SS UNITS  . . .   11.22          3    50.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   17.68         24    75.0    32     CRMSCA  
     SURFACE . . . . . . . .   16.17         43    79.6    54     CRMSCA  
     BURIED  . . . . . . . .   10.24         16    72.7    22     CRMSCA  
     CORE  . . . . . . . . .   12.45         35    79.5    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.84        289    77.9   371     CRMSMC  
     WELL ORDERED  . . . . .   14.84        289    77.9   371     CRMSMC  
     NO INTER CONTACTS . . .   14.84        289    77.9   371     CRMSMC  
     SHIFTED CHAIN . . . . .   15.07        259    76.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .   15.66         15    60.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   13.06        103    77.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .   11.30         15    50.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.75        117    76.0   154     CRMSMC  
     SURFACE . . . . . . . .   16.13        212    80.3   264     CRMSMC  
     BURIED  . . . . . . . .   10.50         77    72.0   107     CRMSMC  
     CORE  . . . . . . . . .   12.49        172    79.3   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   15.42         53    18.7   284     CRMSSC  
     WELL ORDERED  . . . . .   15.42         53    18.7   284     CRMSSC  
     NO INTER CONTACTS . . .   15.42         53    18.7   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   15.42         53    22.1   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   13.95         19    19.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   18.59         21    18.8   112     CRMSSC  
     SURFACE . . . . . . . .   16.53         40    18.0   222     CRMSSC  
     BURIED  . . . . . . . .   11.35         13    21.0    62     CRMSSC  
     CORE  . . . . . . . . .   12.92         32    18.6   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.84        289    49.1   588     CRMSALL 
     WELL ORDERED  . . . . .   14.84        289    49.1   588     CRMSALL 
     NO INTER CONTACTS . . .   14.84        289    49.1   588     CRMSALL 
     SHIFTED CHAIN . . . . .   15.07        259    47.8   542     CRMSALL 
     ALTERNATIVE PARENT  . .   15.66         15    33.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   13.06        103    49.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   17.75        117    48.8   240     CRMSALL 
     SURFACE . . . . . . . .   16.13        212    48.4   438     CRMSALL 
     BURIED  . . . . . . . .   10.50         77    51.3   150     CRMSALL 
     CORE  . . . . . . . . .   12.49        172    49.4   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    29.30      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     5.08      1    33.3     3      26-GGG-28   
 CA  LOOP  3     7.87      7    70.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    19.21      1    25.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    29.31     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     4.92      4    33.3    12      26-GGG-28   
 MC  LOOP  3     7.90     35    70.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    19.25      5    26.3    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    29.31     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     4.92      4    33.3    12      26-GGG-28   
 ALL LOOP  3     7.90     35    40.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    19.25      5    14.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.97      7   100.0     7       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 CA  LOOP  3     2.58      7    70.0    10      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.25     34   100.0    34       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 MC  LOOP  3     3.01     35    70.0    50      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.25     34    64.2    53       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 ALL LOOP  3     3.01     35    40.2    87      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 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 . . . . . . . . . .   12.494      1.000       0.500     59    77.6    76     ERRCA  
     WELL ORDERED  . . . . .   12.494      1.000       0.500     59    77.6    76     ERRCA  
     NO INTER CONTACTS . . .   12.494      1.000       0.500     59    77.6    76     ERRCA  
     SHIFTED CHAIN . . . . .   12.527      1.000       0.500     53    75.7    70     ERRCA  
     ALTERNATIVE PARENT  . .   15.232      1.000       0.500      3    60.0     5     ERRCA  
     SECONDARY STRUCTURE . .   12.473      1.000       0.500     21    77.8    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   14.115      1.000       0.500     24    75.0    32     ERRCA  
     SURFACE . . . . . . . .   13.636      1.000       0.500     43    79.6    54     ERRCA  
     BURIED  . . . . . . . .    9.426      1.000       0.500     16    72.7    22     ERRCA  
     CORE  . . . . . . . . .   11.383      1.000       0.500     35    79.5    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.575      1.000       0.500    289    77.9   371     ERRMC  
     WELL ORDERED  . . . . .   12.575      1.000       0.500    289    77.9   371     ERRMC  
     NO INTER CONTACTS . . .   12.575      1.000       0.500    289    77.9   371     ERRMC  
     SHIFTED CHAIN . . . . .   12.590      1.000       0.500    259    76.0   341     ERRMC  
     ALTERNATIVE PARENT  . .   14.906      1.000       0.500     15    60.0    25     ERRMC  
     SECONDARY STRUCTURE . .   12.517      1.000       0.500    103    77.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   14.252      1.000       0.500    117    76.0   154     ERRMC  
     SURFACE . . . . . . . .   13.617      1.000       0.500    212    80.3   264     ERRMC  
     BURIED  . . . . . . . .    9.705      1.000       0.500     77    72.0   107     ERRMC  
     CORE  . . . . . . . . .   11.434      1.000       0.500    172    79.3   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.244      1.000       0.500     53    18.7   284     ERRSC  
     WELL ORDERED  . . . . .   13.244      1.000       0.500     53    18.7   284     ERRSC  
     NO INTER CONTACTS . . .   13.244      1.000       0.500     53    18.7   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.244      1.000       0.500     53    22.1   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   13.335      1.000       0.500     47    17.9   262     ERRSC  
     ALTERNATIVE PARENT  . .   15.826      1.000       0.500      3    12.0    25     ERRSC  
     SECONDARY STRUCTURE . .   13.249      1.000       0.500     19    19.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   15.210      1.000       0.500     21    18.8   112     ERRSC  
     SURFACE . . . . . . . .   14.130      1.000       0.500     40    18.0   222     ERRSC  
     BURIED  . . . . . . . .   10.520      1.000       0.500     13    21.0    62     ERRSC  
     CORE  . . . . . . . . .   11.955      1.000       0.500     32    18.6   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.575      1.000       0.500    289    49.1   588     ERRALL 
     WELL ORDERED  . . . . .   12.575      1.000       0.500    289    49.1   588     ERRALL 
     NO INTER CONTACTS . . .   12.575      1.000       0.500    289    49.1   588     ERRALL 
     SHIFTED CHAIN . . . . .   12.590      1.000       0.500    259    47.8   542     ERRALL 
     ALTERNATIVE PARENT  . .   14.906      1.000       0.500     15    33.3    45     ERRALL 
     SECONDARY STRUCTURE . .   12.517      1.000       0.500    103    49.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   14.252      1.000       0.500    117    48.8   240     ERRALL 
     SURFACE . . . . . . . .   13.617      1.000       0.500    212    48.4   438     ERRALL 
     BURIED  . . . . . . . .    9.705      1.000       0.500     77    51.3   150     ERRALL 
     CORE  . . . . . . . . .   11.434      1.000       0.500    172    49.4   348     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         2         5         8        27      59      76   DISTCA 
CA  (P)      0.00      2.63      6.58     10.53     35.53              76   DISTCA 
CA  (RMS)    0.00      1.52      1.97      2.94      6.95                   DISTCA 
 
ALL (N)         2         7        22        39       123     289     588   DISTALL 
ALL (P)      0.34      1.19      3.74      6.63     20.92             588   DISTALL 
ALL (RMS)    0.74      1.29      2.13      3.17      6.75                   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)          44            35            24          RMSLSI 
CA  (P)       57.89         46.05         31.58          RMSLSI 
CA  (RMS)      1.67         12.45         17.68          RMSLSI 
 
 
 
END of the results output 
