 
####################################################### 
#                                                     # 
#                        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 452 atoms, 395 common with TARGET 
           Number of atoms possible to evaluate: 320 
 
 
 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 . . . . . . . . . .    81.05           35.6   132    88.0   150     ARMSMC  
     WELL ORDERED  . . . . .    81.05           35.6   132    88.0   150     ARMSMC  
     NO INTER CONTACTS . . .    81.05           35.6   132    88.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    80.69           35.2   122    88.4   138     ARMSMC  
     ALTERNATIVE PARENT  . .    94.92           33.3     6    60.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    79.33           41.3    46    85.2    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    87.34           32.1    56    90.3    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    81.93           35.1    94    88.7   106     ARMSMC  
     BURIED  . . . . . . . .    78.83           36.8    38    86.4    44     ARMSMC  
     CORE  . . . . . . . . .    76.08           38.2    76    86.4    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) =  -0.45726     r(1,2) =  -0.59237     r(1,3) =  -0.66333 
 r(2,1) =  -0.71534     r(2,2) =   0.68815     r(2,3) =  -0.12141 
 r(3,1) =   0.52839     r(3,2) =   0.41899     r(3,3) =  -0.73841 
THE OFFSET VECTOR: 
 v(1) =  99.31841     v(2) =  52.86415     v(3) =  18.20154 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.97           (Number of atoms:   10) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.47         67    88.2    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2160                            CRMSCA  
     WELL ORDERED  . . . . .   14.47         67    88.2    76     CRMSCA  
     NO INTER CONTACTS . . .   14.47         67    88.2    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.19         62    88.6    70     CRMSCA  
     ALTERNATIVE PARENT  . .   15.18          3    60.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   15.49         23    85.2    27     CRMSCA  
     SHIFTED SS UNITS  . . .    4.64          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.05         29    90.6    32     CRMSCA  
     SURFACE . . . . . . . .   15.17         48    88.9    54     CRMSCA  
     BURIED  . . . . . . . .   12.54         19    86.4    22     CRMSCA  
     CORE  . . . . . . . . .   13.14         38    86.4    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.35        320    86.3   371     CRMSMC  
     WELL ORDERED  . . . . .   14.35        320    86.3   371     CRMSMC  
     NO INTER CONTACTS . . .   14.35        320    86.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   14.06        296    86.8   341     CRMSMC  
     ALTERNATIVE PARENT  . .   15.36         14    56.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   15.51        110    82.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .    4.57         28    93.3    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   15.80        136    88.3   154     CRMSMC  
     SURFACE . . . . . . . .   15.04        231    87.5   264     CRMSMC  
     BURIED  . . . . . . . .   12.39         89    83.2   107     CRMSMC  
     CORE  . . . . . . . . .   13.18        184    84.8   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   14.24         52    18.3   284     CRMSSC  
     WELL ORDERED  . . . . .   14.24         52    18.3   284     CRMSSC  
     NO INTER CONTACTS . . .   14.24         52    18.3   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.24         52    21.7   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   15.97         18    18.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   15.33         20    17.9   112     CRMSSC  
     SURFACE . . . . . . . .   14.63         39    17.6   222     CRMSSC  
     BURIED  . . . . . . . .   13.01         13    21.0    62     CRMSSC  
     CORE  . . . . . . . . .   13.52         32    18.6   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.35        320    54.4   588     CRMSALL 
     WELL ORDERED  . . . . .   14.35        320    54.4   588     CRMSALL 
     NO INTER CONTACTS . . .   14.35        320    54.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.06        296    54.6   542     CRMSALL 
     ALTERNATIVE PARENT  . .   15.36         14    31.1    45     CRMSALL 
     SECONDARY STRUCTURE . .   15.51        110    53.1   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   15.80        136    56.7   240     CRMSALL 
     SURFACE . . . . . . . .   15.04        231    52.7   438     CRMSALL 
     BURIED  . . . . . . . .   12.39         89    59.3   150     CRMSALL 
     CORE  . . . . . . . . .   13.18        184    52.9   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    28.63      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     8.53      3   100.0     3      26-GGG-28   
 CA  LOOP  3     8.03     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     5.21      3    75.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    28.32     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2     8.09     12   100.0    12      26-GGG-28   
 MC  LOOP  3     8.09     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     5.12     14    73.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    28.32     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2     8.09     12   100.0    12      26-GGG-28   
 ALL LOOP  3     8.09     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     5.12     14    40.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.28      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.13      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.78     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.08      3    75.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.68     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2     1.15     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.99     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.72     14    73.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.68     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2     1.15     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.99     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.72     14    40.0    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 . . . . . . . . . .   11.694      1.000       0.500     67    88.2    76     ERRCA  
     WELL ORDERED  . . . . .   11.694      1.000       0.500     67    88.2    76     ERRCA  
     NO INTER CONTACTS . . .   11.694      1.000       0.500     67    88.2    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.351      1.000       0.500     62    88.6    70     ERRCA  
     ALTERNATIVE PARENT  . .   10.170      1.000       0.500      3    60.0     5     ERRCA  
     SECONDARY STRUCTURE . .   12.851      1.000       0.500     23    85.2    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   12.582      1.000       0.500     29    90.6    32     ERRCA  
     SURFACE . . . . . . . .   12.083      1.000       0.500     48    88.9    54     ERRCA  
     BURIED  . . . . . . . .   10.711      1.000       0.500     19    86.4    22     ERRCA  
     CORE  . . . . . . . . .   11.016      1.000       0.500     38    86.4    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.607      1.000       0.500    320    86.3   371     ERRMC  
     WELL ORDERED  . . . . .   11.607      1.000       0.500    320    86.3   371     ERRMC  
     NO INTER CONTACTS . . .   11.607      1.000       0.500    320    86.3   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.252      1.000       0.500    296    86.8   341     ERRMC  
     ALTERNATIVE PARENT  . .   10.383      1.000       0.500     14    56.0    25     ERRMC  
     SECONDARY STRUCTURE . .   12.863      1.000       0.500    110    82.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   12.344      1.000       0.500    136    88.3   154     ERRMC  
     SURFACE . . . . . . . .   12.016      1.000       0.500    231    87.5   264     ERRMC  
     BURIED  . . . . . . . .   10.543      1.000       0.500     89    83.2   107     ERRMC  
     CORE  . . . . . . . . .   11.062      1.000       0.500    184    84.8   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.836      1.000       0.500     52    18.3   284     ERRSC  
     WELL ORDERED  . . . . .   11.836      1.000       0.500     52    18.3   284     ERRSC  
     NO INTER CONTACTS . . .   11.836      1.000       0.500     52    18.3   284     ERRSC  
     RELIABLE SIDE CHAINS  .   11.836      1.000       0.500     52    21.7   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   11.628      1.000       0.500     48    18.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   15.119      1.000       0.500      2     8.0    25     ERRSC  
     SECONDARY STRUCTURE . .   13.671      1.000       0.500     18    18.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.267      1.000       0.500     20    17.9   112     ERRSC  
     SURFACE . . . . . . . .   11.985      1.000       0.500     39    17.6   222     ERRSC  
     BURIED  . . . . . . . .   11.390      1.000       0.500     13    21.0    62     ERRSC  
     CORE  . . . . . . . . .   11.566      1.000       0.500     32    18.6   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.607      1.000       0.500    320    54.4   588     ERRALL 
     WELL ORDERED  . . . . .   11.607      1.000       0.500    320    54.4   588     ERRALL 
     NO INTER CONTACTS . . .   11.607      1.000       0.500    320    54.4   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.252      1.000       0.500    296    54.6   542     ERRALL 
     ALTERNATIVE PARENT  . .   10.383      1.000       0.500     14    31.1    45     ERRALL 
     SECONDARY STRUCTURE . .   12.863      1.000       0.500    110    53.1   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   12.344      1.000       0.500    136    56.7   240     ERRALL 
     SURFACE . . . . . . . .   12.016      1.000       0.500    231    52.7   438     ERRALL 
     BURIED  . . . . . . . .   10.543      1.000       0.500     89    59.3   150     ERRALL 
     CORE  . . . . . . . . .   11.062      1.000       0.500    184    52.9   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         5        11        12        39      67      76   DISTCA 
CA  (P)      0.00      6.58     14.47     15.79     51.32              76   DISTCA 
CA  (RMS)    0.00      1.74      2.05      2.25      6.56                   DISTCA 
 
ALL (N)         6        28        43        62       187     320     588   DISTALL 
ALL (P)      1.02      4.76      7.31     10.54     31.80             588   DISTALL 
ALL (RMS)    0.56      1.45      1.88      2.72      6.49                   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            38            29          RMSLSI 
CA  (P)       57.89         50.00         38.16          RMSLSI 
CA  (RMS)      1.67         13.14         16.05          RMSLSI 
 
 
 
END of the results output 
