 
####################################################### 
#                                                     # 
#                        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 567 atoms, 510 common with TARGET 
           Number of atoms possible to evaluate: 142 
 
 
 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 . . . . . . . . . .    83.46           27.6    58    38.7   150     ARMSMC  
     WELL ORDERED  . . . . .    83.46           27.6    58    38.7   150     ARMSMC  
     NO INTER CONTACTS . . .    83.46           27.6    58    38.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    87.01           28.0    50    36.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .    25.14           50.0     2    20.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    64.40           33.3    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    93.74           19.0    21    33.9    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.91           20.5    39    36.8   106     ARMSMC  
     BURIED  . . . . . . . .    65.56           42.1    19    43.2    44     ARMSMC  
     CORE  . . . . . . . . .    77.01           32.4    37    42.0    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) =   0.46786     r(1,2) =   0.83816     r(1,3) =   0.28033 
 r(2,1) =   0.87172     r(2,2) =  -0.38536     r(2,3) =  -0.30267 
 r(3,1) =  -0.14566     r(3,2) =   0.38598     r(3,3) =  -0.91094 
THE OFFSET VECTOR: 
 v(1) = -28.79518     v(2) =   9.18664     v(3) =   1.09614 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.58           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   11.57         30    39.5    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3855                            CRMSCA  
     WELL ORDERED  . . . . .   11.57         30    39.5    76     CRMSCA  
     NO INTER CONTACTS . . .   11.57         30    39.5    76     CRMSCA  
     SHIFTED CHAIN . . . . .   12.37         26    37.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .   13.02          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    6.07         15    55.6    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.98         11    34.4    32     CRMSCA  
     SURFACE . . . . . . . .   13.04         20    37.0    54     CRMSCA  
     BURIED  . . . . . . . .    7.83         10    45.5    22     CRMSCA  
     CORE  . . . . . . . . .    6.66         19    43.2    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   11.78        142    38.3   371     CRMSMC  
     WELL ORDERED  . . . . .   11.78        142    38.3   371     CRMSMC  
     NO INTER CONTACTS . . .   11.78        142    38.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   12.58        123    36.1   341     CRMSMC  
     ALTERNATIVE PARENT  . .   12.38          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    6.16         72    54.1   133     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.52         50    32.5   154     CRMSMC  
     SURFACE . . . . . . . .   13.33         95    36.0   264     CRMSMC  
     BURIED  . . . . . . . .    7.72         47    43.9   107     CRMSMC  
     CORE  . . . . . . . . .    6.87         92    42.4   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.61         22     7.7   284     CRMSSC  
     WELL ORDERED  . . . . .   12.61         22     7.7   284     CRMSSC  
     NO INTER CONTACTS . . .   12.61         22     7.7   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   12.61         22     9.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    6.46         12    12.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   21.81          6     5.4   112     CRMSSC  
     SURFACE . . . . . . . .   14.44         15     6.8   222     CRMSSC  
     BURIED  . . . . . . . .    7.27          7    11.3    62     CRMSSC  
     CORE  . . . . . . . . .    6.33         16     9.3   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   11.78        142    24.1   588     CRMSALL 
     WELL ORDERED  . . . . .   11.78        142    24.1   588     CRMSALL 
     NO INTER CONTACTS . . .   11.78        142    24.1   588     CRMSALL 
     SHIFTED CHAIN . . . . .   12.58        123    22.7   542     CRMSALL 
     ALTERNATIVE PARENT  . .   12.38          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    6.16         72    34.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   17.52         50    20.8   240     CRMSALL 
     SURFACE . . . . . . . .   13.33         95    21.7   438     CRMSALL 
     BURIED  . . . . . . . .    7.72         47    31.3   150     CRMSALL 
     CORE  . . . . . . . . .    6.87         92    26.4   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    22.36      6    85.7     7       1-AEIEVGR-7    
 CA  LOOP  2     4.00      3   100.0     3      26-GGG-28   
 CA  LOOP  3     0.00      0     0.0    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    22.41     29    85.3    34       1-AEIEVGR-7    
 MC  LOOP  2     4.45     12   100.0    12      26-GGG-28   
 MC  LOOP  3     0.00      0     0.0    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    22.41     29    54.7    53       1-AEIEVGR-7    
 ALL LOOP  2     4.45     12   100.0    12      26-GGG-28   
 ALL LOOP  3     0.00      0     0.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.87      6    85.7     7       1-AEIEVGR-7    
 CA  LOOP  2     0.64      3   100.0     3      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.60     29    85.3    34       1-AEIEVGR-7    
 MC  LOOP  2     2.00     12   100.0    12      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.60     29    54.7    53       1-AEIEVGR-7    
 ALL LOOP  2     2.00     12   100.0    12      26-GGG-28   
 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 . . . . . . . . . .    8.642      1.000       0.500     30    39.5    76     ERRCA  
     WELL ORDERED  . . . . .    8.642      1.000       0.500     30    39.5    76     ERRCA  
     NO INTER CONTACTS . . .    8.642      1.000       0.500     30    39.5    76     ERRCA  
     SHIFTED CHAIN . . . . .    9.611      1.000       0.500     26    37.1    70     ERRCA  
     ALTERNATIVE PARENT  . .   13.023      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    4.862      1.000       0.500     15    55.6    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   13.953      1.000       0.500     11    34.4    32     ERRCA  
     SURFACE . . . . . . . .    9.660      1.000       0.500     20    37.0    54     ERRCA  
     BURIED  . . . . . . . .    6.604      1.000       0.500     10    45.5    22     ERRCA  
     CORE  . . . . . . . . .    5.567      1.000       0.500     19    43.2    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.918      1.000       0.500    142    38.3   371     ERRMC  
     WELL ORDERED  . . . . .    8.918      1.000       0.500    142    38.3   371     ERRMC  
     NO INTER CONTACTS . . .    8.918      1.000       0.500    142    38.3   371     ERRMC  
     SHIFTED CHAIN . . . . .    9.883      1.000       0.500    123    36.1   341     ERRMC  
     ALTERNATIVE PARENT  . .   12.270      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    5.023      1.000       0.500     72    54.1   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   14.690      1.000       0.500     50    32.5   154     ERRMC  
     SURFACE . . . . . . . .   10.072      1.000       0.500     95    36.0   264     ERRMC  
     BURIED  . . . . . . . .    6.585      1.000       0.500     47    43.9   107     ERRMC  
     CORE  . . . . . . . . .    5.781      1.000       0.500     92    42.4   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.575      1.000       0.500     22     7.7   284     ERRSC  
     WELL ORDERED  . . . . .    9.575      1.000       0.500     22     7.7   284     ERRSC  
     NO INTER CONTACTS . . .    9.575      1.000       0.500     22     7.7   284     ERRSC  
     RELIABLE SIDE CHAINS  .    9.575      1.000       0.500     22     9.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   10.389      1.000       0.500     19     7.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   13.005      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    5.388      1.000       0.500     12    12.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   20.696      1.000       0.500      6     5.4   112     ERRSC  
     SURFACE . . . . . . . .   11.135      1.000       0.500     15     6.8   222     ERRSC  
     BURIED  . . . . . . . .    6.233      1.000       0.500      7    11.3    62     ERRSC  
     CORE  . . . . . . . . .    5.405      1.000       0.500     16     9.3   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.918      1.000       0.500    142    24.1   588     ERRALL 
     WELL ORDERED  . . . . .    8.918      1.000       0.500    142    24.1   588     ERRALL 
     NO INTER CONTACTS . . .    8.918      1.000       0.500    142    24.1   588     ERRALL 
     SHIFTED CHAIN . . . . .    9.883      1.000       0.500    123    22.7   542     ERRALL 
     ALTERNATIVE PARENT  . .   12.270      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    5.023      1.000       0.500     72    34.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   14.690      1.000       0.500     50    20.8   240     ERRALL 
     SURFACE . . . . . . . .   10.072      1.000       0.500     95    21.7   438     ERRALL 
     BURIED  . . . . . . . .    6.585      1.000       0.500     47    31.3   150     ERRALL 
     CORE  . . . . . . . . .    5.781      1.000       0.500     92    26.4   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)         1         7         9        12        20      30      76   DISTCA 
CA  (P)      1.32      9.21     11.84     15.79     26.32              76   DISTCA 
CA  (RMS)    0.79      1.45      1.72      2.63      4.96                   DISTCA 
 
ALL (N)         8        22        37        55        98     142     588   DISTALL 
ALL (P)      1.36      3.74      6.29      9.35     16.67             588   DISTALL 
ALL (RMS)    0.78      1.38      1.93      2.76      5.46                   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            19            11          RMSLSI 
CA  (P)       57.89         25.00         14.47          RMSLSI 
CA  (RMS)      1.67          6.66         16.98          RMSLSI 
 
 
 
END of the results output 
