 
####################################################### 
#                                                     # 
#                        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 572 atoms, 515 common with TARGET 
           Number of atoms possible to evaluate: 108 
 
 
 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 . . . . . . . . . .    68.86           56.2    32    21.3   150     ARMSMC  
     WELL ORDERED  . . . . .    68.86           56.2    32    21.3   150     ARMSMC  
     NO INTER CONTACTS . . .    68.86           56.2    32    21.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    69.60           57.1    28    20.3   138     ARMSMC  
     ALTERNATIVE PARENT  . .    50.71           33.3     3    30.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    54.26           75.0    20    37.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    99.29           25.0     4     6.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    84.93           50.0    18    17.0   106     ARMSMC  
     BURIED  . . . . . . . .    39.57           64.3    14    31.8    44     ARMSMC  
     CORE  . . . . . . . . .    63.33           60.7    28    31.8    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) =   0.54002     r(1,2) =   0.75625     r(1,3) =  -0.36940 
 r(2,1) =   0.45652     r(2,2) =   0.10553     r(2,3) =   0.88343 
 r(3,1) =   0.70708     r(3,2) =  -0.64571     r(3,3) =  -0.28825 
THE OFFSET VECTOR: 
 v(1) = -29.08795     v(2) = -22.94789     v(3) =  -1.19599 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.39           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.11         22    28.9    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4143                            CRMSCA  
     WELL ORDERED  . . . . .    9.11         22    28.9    76     CRMSCA  
     NO INTER CONTACTS . . .    9.11         22    28.9    76     CRMSCA  
     SHIFTED CHAIN . . . . .    9.22         19    27.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .    1.18          2    40.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    8.20         13    48.1    27     CRMSCA  
     SHIFTED SS UNITS  . . .    3.79          3    50.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.34          4    12.5    32     CRMSCA  
     SURFACE . . . . . . . .    9.86         12    22.2    54     CRMSCA  
     BURIED  . . . . . . . .    8.14         10    45.5    22     CRMSCA  
     CORE  . . . . . . . . .    8.54         18    40.9    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.41        108    29.1   371     CRMSMC  
     WELL ORDERED  . . . . .    9.41        108    29.1   371     CRMSMC  
     NO INTER CONTACTS . . .    9.41        108    29.1   371     CRMSMC  
     SHIFTED CHAIN . . . . .    9.46         93    27.3   341     CRMSMC  
     ALTERNATIVE PARENT  . .    1.45         10    40.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    8.54         64    48.1   133     CRMSMC  
     SHIFTED SS UNITS  . . .    4.01         15    50.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.50         20    13.0   154     CRMSMC  
     SURFACE . . . . . . . .   10.08         60    22.7   264     CRMSMC  
     BURIED  . . . . . . . .    8.48         48    44.9   107     CRMSMC  
     CORE  . . . . . . . . .    8.86         88    40.6   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.38         20     7.0   284     CRMSSC  
     WELL ORDERED  . . . . .    9.38         20     7.0   284     CRMSSC  
     NO INTER CONTACTS . . .    9.38         20     7.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.38         20     8.3   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    8.46         12    12.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.62          4     3.6   112     CRMSSC  
     SURFACE . . . . . . . .   10.01         12     5.4   222     CRMSSC  
     BURIED  . . . . . . . .    8.36          8    12.9    62     CRMSSC  
     CORE  . . . . . . . . .    8.73         16     9.3   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.41        108    18.4   588     CRMSALL 
     WELL ORDERED  . . . . .    9.41        108    18.4   588     CRMSALL 
     NO INTER CONTACTS . . .    9.41        108    18.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .    9.46         93    17.2   542     CRMSALL 
     ALTERNATIVE PARENT  . .    1.45         10    22.2    45     CRMSALL 
     SECONDARY STRUCTURE . .    8.54         64    30.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   11.50         20     8.3   240     CRMSALL 
     SURFACE . . . . . . . .   10.08         60    13.7   438     CRMSALL 
     BURIED  . . . . . . . .    8.48         48    32.0   150     CRMSALL 
     CORE  . . . . . . . . .    8.86         88    25.3   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    15.33      1    10.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.90      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     0.00      0     0.0    12      26-GGG-28   
 MC  LOOP  3    14.96      5    10.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.52      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     0.00      0     0.0    12      26-GGG-28   
 ALL LOOP  3    14.96      5     5.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.52      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 . . . . . . . . . .    7.492      1.000       0.500     22    28.9    76     ERRCA  
     WELL ORDERED  . . . . .    7.492      1.000       0.500     22    28.9    76     ERRCA  
     NO INTER CONTACTS . . .    7.492      1.000       0.500     22    28.9    76     ERRCA  
     SHIFTED CHAIN . . . . .    7.637      1.000       0.500     19    27.1    70     ERRCA  
     ALTERNATIVE PARENT  . .    1.154      1.000       0.500      2    40.0     5     ERRCA  
     SECONDARY STRUCTURE . .    6.593      1.000       0.500     13    48.1    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    9.420      1.000       0.500      4    12.5    32     ERRCA  
     SURFACE . . . . . . . .    7.975      1.000       0.500     12    22.2    54     ERRCA  
     BURIED  . . . . . . . .    6.912      1.000       0.500     10    45.5    22     ERRCA  
     CORE  . . . . . . . . .    7.064      1.000       0.500     18    40.9    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.821      1.000       0.500    108    29.1   371     ERRMC  
     WELL ORDERED  . . . . .    7.821      1.000       0.500    108    29.1   371     ERRMC  
     NO INTER CONTACTS . . .    7.821      1.000       0.500    108    29.1   371     ERRMC  
     SHIFTED CHAIN . . . . .    7.884      1.000       0.500     93    27.3   341     ERRMC  
     ALTERNATIVE PARENT  . .    1.330      1.000       0.500     10    40.0    25     ERRMC  
     SECONDARY STRUCTURE . .    6.989      1.000       0.500     64    48.1   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.609      1.000       0.500     20    13.0   154     ERRMC  
     SURFACE . . . . . . . .    8.352      1.000       0.500     60    22.7   264     ERRMC  
     BURIED  . . . . . . . .    7.156      1.000       0.500     48    44.9   107     ERRMC  
     CORE  . . . . . . . . .    7.414      1.000       0.500     88    40.6   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.748      1.000       0.500     20     7.0   284     ERRSC  
     WELL ORDERED  . . . . .    7.748      1.000       0.500     20     7.0   284     ERRSC  
     NO INTER CONTACTS . . .    7.748      1.000       0.500     20     7.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    7.748      1.000       0.500     20     8.3   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    7.909      1.000       0.500     17     6.5   262     ERRSC  
     ALTERNATIVE PARENT  . .    1.167      1.000       0.500      2     8.0    25     ERRSC  
     SECONDARY STRUCTURE . .    6.906      1.000       0.500     12    12.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.885      1.000       0.500      4     3.6   112     ERRSC  
     SURFACE . . . . . . . .    8.146      1.000       0.500     12     5.4   222     ERRSC  
     BURIED  . . . . . . . .    7.151      1.000       0.500      8    12.9    62     ERRSC  
     CORE  . . . . . . . . .    7.214      1.000       0.500     16     9.3   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.821      1.000       0.500    108    18.4   588     ERRALL 
     WELL ORDERED  . . . . .    7.821      1.000       0.500    108    18.4   588     ERRALL 
     NO INTER CONTACTS . . .    7.821      1.000       0.500    108    18.4   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.884      1.000       0.500     93    17.2   542     ERRALL 
     ALTERNATIVE PARENT  . .    1.330      1.000       0.500     10    22.2    45     ERRALL 
     SECONDARY STRUCTURE . .    6.989      1.000       0.500     64    30.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.609      1.000       0.500     20     8.3   240     ERRALL 
     SURFACE . . . . . . . .    8.352      1.000       0.500     60    13.7   438     ERRALL 
     BURIED  . . . . . . . .    7.156      1.000       0.500     48    32.0   150     ERRALL 
     CORE  . . . . . . . . .    7.414      1.000       0.500     88    25.3   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         5         6         9        15      22      76   DISTCA 
CA  (P)      2.63      6.58      7.89     11.84     19.74              76   DISTCA 
CA  (RMS)    0.89      1.16      1.39      2.86      5.36                   DISTCA 
 
ALL (N)         6        21        27        40        72     108     588   DISTALL 
ALL (P)      1.02      3.57      4.59      6.80     12.24             588   DISTALL 
ALL (RMS)    0.84      1.44      1.78      2.78      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            18             4          RMSLSI 
CA  (P)       57.89         23.68          5.26          RMSLSI 
CA  (RMS)      1.67          8.54         11.34          RMSLSI 
 
 
 
END of the results output 
