 
####################################################### 
#                                                     # 
#                        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 558 atoms, 501 common with TARGET 
           Number of atoms possible to evaluate: 151 
 
 
 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 . . . . . . . . . .    99.52            9.6    52    34.7   150     ARMSMC  
     WELL ORDERED  . . . . .    99.52            9.6    52    34.7   150     ARMSMC  
     NO INTER CONTACTS . . .    99.52            9.6    52    34.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    96.84            7.0    43    31.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .   114.33            0.0     7    70.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    99.32           10.8    37    68.5    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   115.43            7.1    14    22.6    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    88.17           13.8    29    27.4   106     ARMSMC  
     BURIED  . . . . . . . .   112.21            4.3    23    52.3    44     ARMSMC  
     CORE  . . . . . . . . .    92.98           10.5    38    43.2    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) =  -0.04027     r(1,2) =   0.97962     r(1,3) =  -0.19677 
 r(2,1) =  -0.75003     r(2,2) =  -0.15975     r(2,3) =  -0.64182 
 r(3,1) =  -0.66017     r(3,2) =   0.12173     r(3,3) =   0.74118 
THE OFFSET VECTOR: 
 v(1) =   2.88611     v(2) =   6.00496     v(3) =   2.78612 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.64           (Number of atoms:   10) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.88         31    40.8    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1896                            CRMSCA  
     WELL ORDERED  . . . . .    5.88         31    40.8    76     CRMSCA  
     NO INTER CONTACTS . . .    5.88         31    40.8    76     CRMSCA  
     SHIFTED CHAIN . . . . .    6.03         26    37.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .    4.78          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    5.18         21    77.8    27     CRMSCA  
     SHIFTED SS UNITS  . . .    6.42          4    66.7     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.50          8    25.0    32     CRMSCA  
     SURFACE . . . . . . . .    6.17         18    33.3    54     CRMSCA  
     BURIED  . . . . . . . .    5.45         13    59.1    22     CRMSCA  
     CORE  . . . . . . . . .    5.65         23    52.3    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.19        151    40.7   371     CRMSMC  
     WELL ORDERED  . . . . .    6.19        151    40.7   371     CRMSMC  
     NO INTER CONTACTS . . .    6.19        151    40.7   371     CRMSMC  
     SHIFTED CHAIN . . . . .    6.35        126    37.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .    5.29         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    5.55        104    78.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .    6.49         20    66.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.95         37    24.0   154     CRMSMC  
     SURFACE . . . . . . . .    6.41         88    33.3   264     CRMSMC  
     BURIED  . . . . . . . .    5.88         63    58.9   107     CRMSMC  
     CORE  . . . . . . . . .    5.93        114    52.5   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    6.48         27     9.5   284     CRMSSC  
     WELL ORDERED  . . . . .    6.48         27     9.5   284     CRMSSC  
     NO INTER CONTACTS . . .    6.48         27     9.5   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    6.48         27    11.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    6.17         20    20.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.14          5     4.5   112     CRMSSC  
     SURFACE . . . . . . . .    6.67         16     7.2   222     CRMSSC  
     BURIED  . . . . . . . .    6.20         11    17.7    62     CRMSSC  
     CORE  . . . . . . . . .    6.32         22    12.8   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.19        151    25.7   588     CRMSALL 
     WELL ORDERED  . . . . .    6.19        151    25.7   588     CRMSALL 
     NO INTER CONTACTS . . .    6.19        151    25.7   588     CRMSALL 
     SHIFTED CHAIN . . . . .    6.35        126    23.2   542     CRMSALL 
     ALTERNATIVE PARENT  . .    5.29         20    44.4    45     CRMSALL 
     SECONDARY STRUCTURE . .    5.55        104    50.2   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.95         37    15.4   240     CRMSALL 
     SURFACE . . . . . . . .    6.41         88    20.1   438     CRMSALL 
     BURIED  . . . . . . . .    5.88         63    42.0   150     CRMSALL 
     CORE  . . . . . . . . .    5.93        114    32.8   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     6.57      2    66.7     3      26-GGG-28   
 CA  LOOP  3     0.00      0     0.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.71      1    25.0     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     7.01      8    66.7    12      26-GGG-28   
 MC  LOOP  3     0.00      0     0.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.22      5    26.3    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     7.01      8    66.7    12      26-GGG-28   
 ALL LOOP  3     0.00      0     0.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.22      5    14.3    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 . . . . . . . . . .    5.099      1.000       0.500     31    40.8    76     ERRCA  
     WELL ORDERED  . . . . .    5.099      1.000       0.500     31    40.8    76     ERRCA  
     NO INTER CONTACTS . . .    5.099      1.000       0.500     31    40.8    76     ERRCA  
     SHIFTED CHAIN . . . . .    5.253      1.000       0.500     26    37.1    70     ERRCA  
     ALTERNATIVE PARENT  . .    3.977      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .    4.483      1.000       0.500     21    77.8    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.924      1.000       0.500      8    25.0    32     ERRCA  
     SURFACE . . . . . . . .    5.426      1.000       0.500     18    33.3    54     ERRCA  
     BURIED  . . . . . . . .    4.645      1.000       0.500     13    59.1    22     ERRCA  
     CORE  . . . . . . . . .    4.812      1.000       0.500     23    52.3    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.378      1.000       0.500    151    40.7   371     ERRMC  
     WELL ORDERED  . . . . .    5.378      1.000       0.500    151    40.7   371     ERRMC  
     NO INTER CONTACTS . . .    5.378      1.000       0.500    151    40.7   371     ERRMC  
     SHIFTED CHAIN . . . . .    5.551      1.000       0.500    126    37.0   341     ERRMC  
     ALTERNATIVE PARENT  . .    4.493      1.000       0.500     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .    4.784      1.000       0.500    104    78.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    6.297      1.000       0.500     37    24.0   154     ERRMC  
     SURFACE . . . . . . . .    5.620      1.000       0.500     88    33.3   264     ERRMC  
     BURIED  . . . . . . . .    5.041      1.000       0.500     63    58.9   107     ERRMC  
     CORE  . . . . . . . . .    5.080      1.000       0.500    114    52.5   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.771      1.000       0.500     27     9.5   284     ERRSC  
     WELL ORDERED  . . . . .    5.771      1.000       0.500     27     9.5   284     ERRSC  
     NO INTER CONTACTS . . .    5.771      1.000       0.500     27     9.5   284     ERRSC  
     RELIABLE SIDE CHAINS  .    5.771      1.000       0.500     27    11.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    5.946      1.000       0.500     22     8.4   262     ERRSC  
     ALTERNATIVE PARENT  . .    4.720      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .    5.554      1.000       0.500     20    20.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.800      1.000       0.500      5     4.5   112     ERRSC  
     SURFACE . . . . . . . .    5.938      1.000       0.500     16     7.2   222     ERRSC  
     BURIED  . . . . . . . .    5.528      1.000       0.500     11    17.7    62     ERRSC  
     CORE  . . . . . . . . .    5.538      1.000       0.500     22    12.8   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.378      1.000       0.500    151    25.7   588     ERRALL 
     WELL ORDERED  . . . . .    5.378      1.000       0.500    151    25.7   588     ERRALL 
     NO INTER CONTACTS . . .    5.378      1.000       0.500    151    25.7   588     ERRALL 
     SHIFTED CHAIN . . . . .    5.551      1.000       0.500    126    23.2   542     ERRALL 
     ALTERNATIVE PARENT  . .    4.493      1.000       0.500     20    44.4    45     ERRALL 
     SECONDARY STRUCTURE . .    4.784      1.000       0.500    104    50.2   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.297      1.000       0.500     37    15.4   240     ERRALL 
     SURFACE . . . . . . . .    5.620      1.000       0.500     88    20.1   438     ERRALL 
     BURIED  . . . . . . . .    5.041      1.000       0.500     63    42.0   150     ERRALL 
     CORE  . . . . . . . . .    5.080      1.000       0.500    114    32.8   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         9        10        14        30      31      76   DISTCA 
CA  (P)      0.00     11.84     13.16     18.42     39.47              76   DISTCA 
CA  (RMS)    0.00      1.56      1.64      2.70      5.56                   DISTCA 
 
ALL (N)         1        32        43        67       139     151     588   DISTALL 
ALL (P)      0.17      5.44      7.31     11.39     23.64             588   DISTALL 
ALL (RMS)    0.65      1.49      1.78      2.87      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            23             8          RMSLSI 
CA  (P)       57.89         30.26         10.53          RMSLSI 
CA  (RMS)      1.67          5.65          6.50          RMSLSI 
 
 
 
END of the results output 
