 
####################################################### 
#                                                     # 
#                        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 557 atoms, 500 common with TARGET 
           Number of atoms possible to evaluate: 138 
 
 
 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 . . . . . . . . . .    61.02           52.3    44    29.3   150     ARMSMC  
     WELL ORDERED  . . . . .    61.02           52.3    44    29.3   150     ARMSMC  
     NO INTER CONTACTS . . .    61.02           52.3    44    29.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    61.68           51.3    39    28.3   138     ARMSMC  
     ALTERNATIVE PARENT  . .    74.97           14.3     7    70.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    49.58           56.7    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    80.34           36.4    11    17.7    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    70.11           58.3    24    22.6   106     ARMSMC  
     BURIED  . . . . . . . .    47.89           45.0    20    45.5    44     ARMSMC  
     CORE  . . . . . . . . .    53.04           57.6    33    37.5    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) =   0.61142     r(1,2) =   0.62171     r(1,3) =  -0.48953 
 r(2,1) =   0.47711     r(2,2) =  -0.78318     r(2,3) =  -0.39874 
 r(3,1) =  -0.63129     r(3,2) =   0.01024     r(3,3) =  -0.77548 
THE OFFSET VECTOR: 
 v(1) = -51.80733     v(2) =   5.79665     v(3) =  78.57313 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.52           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   11.87         28    36.8    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4238                            CRMSCA  
     WELL ORDERED  . . . . .   11.87         28    36.8    76     CRMSCA  
     NO INTER CONTACTS . . .   11.87         28    36.8    76     CRMSCA  
     SHIFTED CHAIN . . . . .   12.11         25    35.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .   15.99          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   11.01         18    66.7    27     CRMSCA  
     SHIFTED SS UNITS  . . .    7.95          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.28          7    21.9    32     CRMSCA  
     SURFACE . . . . . . . .   12.04         16    29.6    54     CRMSCA  
     BURIED  . . . . . . . .   11.63         12    54.5    22     CRMSCA  
     CORE  . . . . . . . . .   12.06         21    47.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   12.00        138    37.2   371     CRMSMC  
     WELL ORDERED  . . . . .   12.00        138    37.2   371     CRMSMC  
     NO INTER CONTACTS . . .   12.00        138    37.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   12.22        124    36.4   341     CRMSMC  
     ALTERNATIVE PARENT  . .   15.94         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   11.13         88    66.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .    7.89         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.28         34    22.1   154     CRMSMC  
     SURFACE . . . . . . . .   12.03         80    30.3   264     CRMSMC  
     BURIED  . . . . . . . .   11.94         58    54.2   107     CRMSMC  
     CORE  . . . . . . . . .   12.22        104    47.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.53         26     9.2   284     CRMSSC  
     WELL ORDERED  . . . . .   12.53         26     9.2   284     CRMSSC  
     NO INTER CONTACTS . . .   12.53         26     9.2   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   12.53         26    10.8   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   11.99         16    16.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   12.69          6     5.4   112     CRMSSC  
     SURFACE . . . . . . . .   12.74         16     7.2   222     CRMSSC  
     BURIED  . . . . . . . .   12.19         10    16.1    62     CRMSSC  
     CORE  . . . . . . . . .   12.48         20    11.6   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   12.00        138    23.5   588     CRMSALL 
     WELL ORDERED  . . . . .   12.00        138    23.5   588     CRMSALL 
     NO INTER CONTACTS . . .   12.00        138    23.5   588     CRMSALL 
     SHIFTED CHAIN . . . . .   12.22        124    22.9   542     CRMSALL 
     ALTERNATIVE PARENT  . .   15.94         20    44.4    45     CRMSALL 
     SECONDARY STRUCTURE . .   11.13         88    42.5   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   11.28         34    14.2   240     CRMSALL 
     SURFACE . . . . . . . .   12.03         80    18.3   438     CRMSALL 
     BURIED  . . . . . . . .   11.94         58    38.7   150     CRMSALL 
     CORE  . . . . . . . . .   12.22        104    29.9   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    13.32      1    10.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    24.83      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    13.00      5    10.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    24.46      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    13.00      5     5.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    24.46      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 . . . . . . . . . .    9.876      1.000       0.500     28    36.8    76     ERRCA  
     WELL ORDERED  . . . . .    9.876      1.000       0.500     28    36.8    76     ERRCA  
     NO INTER CONTACTS . . .    9.876      1.000       0.500     28    36.8    76     ERRCA  
     SHIFTED CHAIN . . . . .    9.979      1.000       0.500     25    35.7    70     ERRCA  
     ALTERNATIVE PARENT  . .   12.029      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .    8.986      1.000       0.500     18    66.7    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    7.979      1.000       0.500      7    21.9    32     ERRCA  
     SURFACE . . . . . . . .    9.770      1.000       0.500     16    29.6    54     ERRCA  
     BURIED  . . . . . . . .   10.018      1.000       0.500     12    54.5    22     ERRCA  
     CORE  . . . . . . . . .   10.509      1.000       0.500     21    47.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.047      1.000       0.500    138    37.2   371     ERRMC  
     WELL ORDERED  . . . . .   10.047      1.000       0.500    138    37.2   371     ERRMC  
     NO INTER CONTACTS . . .   10.047      1.000       0.500    138    37.2   371     ERRMC  
     SHIFTED CHAIN . . . . .   10.158      1.000       0.500    124    36.4   341     ERRMC  
     ALTERNATIVE PARENT  . .   11.950      1.000       0.500     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .    9.132      1.000       0.500     88    66.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    8.102      1.000       0.500     34    22.1   154     ERRMC  
     SURFACE . . . . . . . .    9.888      1.000       0.500     80    30.3   264     ERRMC  
     BURIED  . . . . . . . .   10.266      1.000       0.500     58    54.2   107     ERRMC  
     CORE  . . . . . . . . .   10.683      1.000       0.500    104    47.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.722      1.000       0.500     26     9.2   284     ERRSC  
     WELL ORDERED  . . . . .   10.722      1.000       0.500     26     9.2   284     ERRSC  
     NO INTER CONTACTS . . .   10.722      1.000       0.500     26     9.2   284     ERRSC  
     RELIABLE SIDE CHAINS  .   10.722      1.000       0.500     26    10.8   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   10.957      1.000       0.500     24     9.2   262     ERRSC  
     ALTERNATIVE PARENT  . .   12.827      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .   10.087      1.000       0.500     16    16.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.705      1.000       0.500      6     5.4   112     ERRSC  
     SURFACE . . . . . . . .   10.626      1.000       0.500     16     7.2   222     ERRSC  
     BURIED  . . . . . . . .   10.876      1.000       0.500     10    16.1    62     ERRSC  
     CORE  . . . . . . . . .   11.027      1.000       0.500     20    11.6   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.047      1.000       0.500    138    23.5   588     ERRALL 
     WELL ORDERED  . . . . .   10.047      1.000       0.500    138    23.5   588     ERRALL 
     NO INTER CONTACTS . . .   10.047      1.000       0.500    138    23.5   588     ERRALL 
     SHIFTED CHAIN . . . . .   10.158      1.000       0.500    124    22.9   542     ERRALL 
     ALTERNATIVE PARENT  . .   11.950      1.000       0.500     20    44.4    45     ERRALL 
     SECONDARY STRUCTURE . .    9.132      1.000       0.500     88    42.5   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    8.102      1.000       0.500     34    14.2   240     ERRALL 
     SURFACE . . . . . . . .    9.888      1.000       0.500     80    18.3   438     ERRALL 
     BURIED  . . . . . . . .   10.266      1.000       0.500     58    38.7   150     ERRALL 
     CORE  . . . . . . . . .   10.683      1.000       0.500    104    29.9   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         6         6         9        14      28      76   DISTCA 
CA  (P)      0.00      7.89      7.89     11.84     18.42              76   DISTCA 
CA  (RMS)    0.00      1.52      1.52      2.76      5.28                   DISTCA 
 
ALL (N)         5        17        25        42        71     138     588   DISTALL 
ALL (P)      0.85      2.89      4.25      7.14     12.07             588   DISTALL 
ALL (RMS)    0.71      1.35      1.87      2.96      5.55                   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            21             7          RMSLSI 
CA  (P)       57.89         27.63          9.21          RMSLSI 
CA  (RMS)      1.67         12.06         11.28          RMSLSI 
 
 
 
END of the results output 
