 
####################################################### 
#                                                     # 
#                        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 591 atoms, 534 common with TARGET 
           Number of atoms possible to evaluate: 88 
 
 
 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 . . . . . . . . . .    67.14           50.0    24    16.0   150     ARMSMC  
     WELL ORDERED  . . . . .    67.14           50.0    24    16.0   150     ARMSMC  
     NO INTER CONTACTS . . .    67.14           50.0    24    16.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    64.36           55.0    20    14.5   138     ARMSMC  
     ALTERNATIVE PARENT  . .    66.93            0.0     1    10.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    61.56           50.0    20    37.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   116.35           50.0     2     3.2    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    89.10           33.3    12    11.3   106     ARMSMC  
     BURIED  . . . . . . . .    32.81           66.7    12    27.3    44     ARMSMC  
     CORE  . . . . . . . . .    60.72           50.0    22    25.0    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) =  -0.29099     r(1,2) =   0.28703     r(1,3) =  -0.91266 
 r(2,1) =  -0.79865     r(2,2) =  -0.59811     r(2,3) =   0.06654 
 r(3,1) =  -0.52677     r(3,2) =   0.74825     r(3,3) =   0.40328 
THE OFFSET VECTOR: 
 v(1) =  -1.30794     v(2) =  26.50348     v(3) = -23.63677 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.55           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.83         18    23.7    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4904                            CRMSCA  
     WELL ORDERED  . . . . .    8.83         18    23.7    76     CRMSCA  
     NO INTER CONTACTS . . .    8.83         18    23.7    76     CRMSCA  
     SHIFTED CHAIN . . . . .    8.48         15    21.4    70     CRMSCA  
     ALTERNATIVE PARENT  . .    1.11          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    9.39         13    48.1    27     CRMSCA  
     SHIFTED SS UNITS  . . .    7.13          2    33.3     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   14.52          2     6.2    32     CRMSCA  
     SURFACE . . . . . . . .   10.18          8    14.8    54     CRMSCA  
     BURIED  . . . . . . . .    7.58         10    45.5    22     CRMSCA  
     CORE  . . . . . . . . .    7.83         16    36.4    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.18         88    23.7   371     CRMSMC  
     WELL ORDERED  . . . . .    9.18         88    23.7   371     CRMSMC  
     NO INTER CONTACTS . . .    9.18         88    23.7   371     CRMSMC  
     SHIFTED CHAIN . . . . .    8.70         73    21.4   341     CRMSMC  
     ALTERNATIVE PARENT  . .    2.75          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    9.68         64    48.1   133     CRMSMC  
     SHIFTED SS UNITS  . . .    6.99         10    33.3    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   14.55         10     6.5   154     CRMSMC  
     SURFACE . . . . . . . .   10.45         40    15.2   264     CRMSMC  
     BURIED  . . . . . . . .    7.97         48    44.9   107     CRMSMC  
     CORE  . . . . . . . . .    8.24         78    35.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.14         16     5.6   284     CRMSSC  
     WELL ORDERED  . . . . .    9.14         16     5.6   284     CRMSSC  
     NO INTER CONTACTS . . .    9.14         16     5.6   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.14         16     6.7   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    9.65         12    12.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.90          2     1.8   112     CRMSSC  
     SURFACE . . . . . . . .   10.45          8     3.6   222     CRMSSC  
     BURIED  . . . . . . . .    7.61          8    12.9    62     CRMSSC  
     CORE  . . . . . . . . .    8.24         14     8.1   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.18         88    15.0   588     CRMSALL 
     WELL ORDERED  . . . . .    9.18         88    15.0   588     CRMSALL 
     NO INTER CONTACTS . . .    9.18         88    15.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.70         73    13.5   542     CRMSALL 
     ALTERNATIVE PARENT  . .    2.75          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    9.68         64    30.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   14.55         10     4.2   240     CRMSALL 
     SURFACE . . . . . . . .   10.45         40     9.1   438     CRMSALL 
     BURIED  . . . . . . . .    7.97         48    32.0   150     CRMSALL 
     CORE  . . . . . . . . .    8.24         78    22.4   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.00      0     0.0     3      26-GGG-28   
 CA  LOOP  3    10.06      1    10.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.00      0     0.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    34       1-AEIEVGR-7    
 MC  LOOP  2     0.00      0     0.0    12      26-GGG-28   
 MC  LOOP  3     9.67      5    10.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     0.00      0     0.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    53       1-AEIEVGR-7    
 ALL LOOP  2     0.00      0     0.0    12      26-GGG-28   
 ALL LOOP  3     9.67      5     5.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 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). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 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). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 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). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 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 . . . . . . . . . .    7.054      1.000       0.500     18    23.7    76     ERRCA  
     WELL ORDERED  . . . . .    7.054      1.000       0.500     18    23.7    76     ERRCA  
     NO INTER CONTACTS . . .    7.054      1.000       0.500     18    23.7    76     ERRCA  
     SHIFTED CHAIN . . . . .    6.925      1.000       0.500     15    21.4    70     ERRCA  
     ALTERNATIVE PARENT  . .    1.108      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    7.292      1.000       0.500     13    48.1    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   13.981      1.000       0.500      2     6.2    32     ERRCA  
     SURFACE . . . . . . . .    8.618      1.000       0.500      8    14.8    54     ERRCA  
     BURIED  . . . . . . . .    5.804      1.000       0.500     10    45.5    22     ERRCA  
     CORE  . . . . . . . . .    6.188      1.000       0.500     16    36.4    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.488      1.000       0.500     88    23.7   371     ERRMC  
     WELL ORDERED  . . . . .    7.488      1.000       0.500     88    23.7   371     ERRMC  
     NO INTER CONTACTS . . .    7.488      1.000       0.500     88    23.7   371     ERRMC  
     SHIFTED CHAIN . . . . .    7.219      1.000       0.500     73    21.4   341     ERRMC  
     ALTERNATIVE PARENT  . .    2.467      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    7.679      1.000       0.500     64    48.1   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   13.880      1.000       0.500     10     6.5   154     ERRMC  
     SURFACE . . . . . . . .    8.989      1.000       0.500     40    15.2   264     ERRMC  
     BURIED  . . . . . . . .    6.237      1.000       0.500     48    44.9   107     ERRMC  
     CORE  . . . . . . . . .    6.669      1.000       0.500     78    35.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.718      1.000       0.500     16     5.6   284     ERRSC  
     WELL ORDERED  . . . . .    7.718      1.000       0.500     16     5.6   284     ERRSC  
     NO INTER CONTACTS . . .    7.718      1.000       0.500     16     5.6   284     ERRSC  
     RELIABLE SIDE CHAINS  .    7.718      1.000       0.500     16     6.7   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    7.525      1.000       0.500     13     5.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    3.730      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    7.960      1.000       0.500     12    12.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   13.498      1.000       0.500      2     1.8   112     ERRSC  
     SURFACE . . . . . . . .    9.204      1.000       0.500      8     3.6   222     ERRSC  
     BURIED  . . . . . . . .    6.232      1.000       0.500      8    12.9    62     ERRSC  
     CORE  . . . . . . . . .    6.892      1.000       0.500     14     8.1   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.488      1.000       0.500     88    15.0   588     ERRALL 
     WELL ORDERED  . . . . .    7.488      1.000       0.500     88    15.0   588     ERRALL 
     NO INTER CONTACTS . . .    7.488      1.000       0.500     88    15.0   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.219      1.000       0.500     73    13.5   542     ERRALL 
     ALTERNATIVE PARENT  . .    2.467      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    7.679      1.000       0.500     64    30.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   13.880      1.000       0.500     10     4.2   240     ERRALL 
     SURFACE . . . . . . . .    8.989      1.000       0.500     40     9.1   438     ERRALL 
     BURIED  . . . . . . . .    6.237      1.000       0.500     48    32.0   150     ERRALL 
     CORE  . . . . . . . . .    6.669      1.000       0.500     78    22.4   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)         2         4         6         7        13      18      76   DISTCA 
CA  (P)      2.63      5.26      7.89      9.21     17.11              76   DISTCA 
CA  (RMS)    0.81      1.16      1.55      2.34      5.21                   DISTCA 
 
ALL (N)         3        12        23        37        64      88     588   DISTALL 
ALL (P)      0.51      2.04      3.91      6.29     10.88             588   DISTALL 
ALL (RMS)    0.81      1.36      1.99      3.03      5.52                   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            16             2          RMSLSI 
CA  (P)       57.89         21.05          2.63          RMSLSI 
CA  (RMS)      1.67          7.83         14.52          RMSLSI 
 
 
 
END of the results output 
