 
####################################################### 
#                                                     # 
#                        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 446 atoms, 389 common with TARGET 
           Number of atoms possible to evaluate: 331 
 
 
 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 . . . . . . . . . .    86.56           34.1   132    88.0   150     ARMSMC  
     WELL ORDERED  . . . . .    86.56           34.1   132    88.0   150     ARMSMC  
     NO INTER CONTACTS . . .    86.56           34.1   132    88.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    87.43           33.6   128    92.8   138     ARMSMC  
     ALTERNATIVE PARENT  . .    73.16           20.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    61.63           52.6    38    70.4    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   100.68           29.5    61    98.4    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    92.15           30.9    94    88.7   106     ARMSMC  
     BURIED  . . . . . . . .    70.83           42.1    38    86.4    44     ARMSMC  
     CORE  . . . . . . . . .    72.25           38.0    71    80.7    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) =   0.27638     r(1,2) =  -0.23630     r(1,3) =  -0.93154 
 r(2,1) =  -0.95348     r(2,2) =  -0.18883     r(2,3) =  -0.23500 
 r(3,1) =  -0.12037     r(3,2) =   0.95316     r(3,3) =  -0.27749 
THE OFFSET VECTOR: 
 v(1) =  -7.83714     v(2) =  99.72545     v(3) = -14.25381 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.73           (Number of atoms:   10) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   13.12         69    90.8    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1902                            CRMSCA  
     WELL ORDERED  . . . . .   13.12         69    90.8    76     CRMSCA  
     NO INTER CONTACTS . . .   13.12         69    90.8    76     CRMSCA  
     SHIFTED CHAIN . . . . .   13.24         67    95.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .    8.87          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   10.09         20    74.1    27     CRMSCA  
     SHIFTED SS UNITS  . . .    6.54          5    83.3     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   13.44         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .   13.74         49    90.7    54     CRMSCA  
     BURIED  . . . . . . . .   11.47         20    90.9    22     CRMSCA  
     CORE  . . . . . . . . .   12.84         37    84.1    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.12        331    89.2   371     CRMSMC  
     WELL ORDERED  . . . . .   13.12        331    89.2   371     CRMSMC  
     NO INTER CONTACTS . . .   13.12        331    89.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.23        321    94.1   341     CRMSMC  
     ALTERNATIVE PARENT  . .    8.79         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   10.12         97    72.9   133     CRMSMC  
     SHIFTED SS UNITS  . . .    6.47         24    80.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   13.47        151    98.1   154     CRMSMC  
     SURFACE . . . . . . . .   13.78        235    89.0   264     CRMSMC  
     BURIED  . . . . . . . .   11.34         96    89.7   107     CRMSMC  
     CORE  . . . . . . . . .   12.81        180    82.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.52         55    19.4   284     CRMSSC  
     WELL ORDERED  . . . . .   13.52         55    19.4   284     CRMSSC  
     NO INTER CONTACTS . . .   13.52         55    19.4   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.52         55    22.9   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   10.40         17    17.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.94         23    20.5   112     CRMSSC  
     SURFACE . . . . . . . .   14.52         39    17.6   222     CRMSSC  
     BURIED  . . . . . . . .   10.67         16    25.8    62     CRMSSC  
     CORE  . . . . . . . . .   13.20         32    18.6   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.12        331    56.3   588     CRMSALL 
     WELL ORDERED  . . . . .   13.12        331    56.3   588     CRMSALL 
     NO INTER CONTACTS . . .   13.12        331    56.3   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.23        321    59.2   542     CRMSALL 
     ALTERNATIVE PARENT  . .    8.79         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   10.12         97    46.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   13.47        151    62.9   240     CRMSALL 
     SURFACE . . . . . . . .   13.78        235    53.7   438     CRMSALL 
     BURIED  . . . . . . . .   11.34         96    64.0   150     CRMSALL 
     CORE  . . . . . . . . .   12.81        180    51.7   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    11.86      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2    10.73      3   100.0     3      26-GGG-28   
 CA  LOOP  3    16.88     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     3.12      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    11.87     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2    10.63     12   100.0    12      26-GGG-28   
 MC  LOOP  3    16.93     48    96.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     3.08     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    11.87     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2    10.63     12   100.0    12      26-GGG-28   
 ALL LOOP  3    16.93     48    55.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     3.08     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.36      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.06      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.74     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.48      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.78     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.93     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.86     48    96.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.77     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.78     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     1.93     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.86     48    55.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.77     18    51.4    35      65-RQGR-68   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.276      1.000       0.500     69    90.8    76     ERRCA  
     WELL ORDERED  . . . . .   11.276      1.000       0.500     69    90.8    76     ERRCA  
     NO INTER CONTACTS . . .   11.276      1.000       0.500     69    90.8    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.422      1.000       0.500     67    95.7    70     ERRCA  
     ALTERNATIVE PARENT  . .    6.768      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    8.476      1.000       0.500     20    74.1    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.405      1.000       0.500     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .   11.914      1.000       0.500     49    90.7    54     ERRCA  
     BURIED  . . . . . . . .    9.711      1.000       0.500     20    90.9    22     ERRCA  
     CORE  . . . . . . . . .   11.164      1.000       0.500     37    84.1    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.286      1.000       0.500    331    89.2   371     ERRMC  
     WELL ORDERED  . . . . .   11.286      1.000       0.500    331    89.2   371     ERRMC  
     NO INTER CONTACTS . . .   11.286      1.000       0.500    331    89.2   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.430      1.000       0.500    321    94.1   341     ERRMC  
     ALTERNATIVE PARENT  . .    6.809      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    8.528      1.000       0.500     97    72.9   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   11.458      1.000       0.500    151    98.1   154     ERRMC  
     SURFACE . . . . . . . .   11.984      1.000       0.500    235    89.0   264     ERRMC  
     BURIED  . . . . . . . .    9.577      1.000       0.500     96    89.7   107     ERRMC  
     CORE  . . . . . . . . .   11.141      1.000       0.500    180    82.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.639      1.000       0.500     55    19.4   284     ERRSC  
     WELL ORDERED  . . . . .   11.639      1.000       0.500     55    19.4   284     ERRSC  
     NO INTER CONTACTS . . .   11.639      1.000       0.500     55    19.4   284     ERRSC  
     RELIABLE SIDE CHAINS  .   11.639      1.000       0.500     55    22.9   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   11.865      1.000       0.500     53    20.2   262     ERRSC  
     ALTERNATIVE PARENT  . .    7.331      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .    8.840      1.000       0.500     17    17.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   11.777      1.000       0.500     23    20.5   112     ERRSC  
     SURFACE . . . . . . . .   12.672      1.000       0.500     39    17.6   222     ERRSC  
     BURIED  . . . . . . . .    9.122      1.000       0.500     16    25.8    62     ERRSC  
     CORE  . . . . . . . . .   11.540      1.000       0.500     32    18.6   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.286      1.000       0.500    331    56.3   588     ERRALL 
     WELL ORDERED  . . . . .   11.286      1.000       0.500    331    56.3   588     ERRALL 
     NO INTER CONTACTS . . .   11.286      1.000       0.500    331    56.3   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.430      1.000       0.500    321    59.2   542     ERRALL 
     ALTERNATIVE PARENT  . .    6.809      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .    8.528      1.000       0.500     97    46.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   11.458      1.000       0.500    151    62.9   240     ERRALL 
     SURFACE . . . . . . . .   11.984      1.000       0.500    235    53.7   438     ERRALL 
     BURIED  . . . . . . . .    9.577      1.000       0.500     96    64.0   150     ERRALL 
     CORE  . . . . . . . . .   11.141      1.000       0.500    180    51.7   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)         3         7        10        16        32      69      76   DISTCA 
CA  (P)      3.95      9.21     13.16     21.05     42.11              76   DISTCA 
CA  (RMS)    0.93      1.43      1.73      2.84      5.70                   DISTCA 
 
ALL (N)         9        28        50        82       151     331     588   DISTALL 
ALL (P)      1.53      4.76      8.50     13.95     25.68             588   DISTALL 
ALL (RMS)    0.85      1.40      1.93      2.99      5.66                   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            37            32          RMSLSI 
CA  (P)       57.89         48.68         42.11          RMSLSI 
CA  (RMS)      1.67         12.84         13.44          RMSLSI 
 
 
 
END of the results output 
