 
####################################################### 
#                                                     # 
#                        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 402 atoms, 363 common with TARGET 
           Number of atoms possible to evaluate: 346 
 
 
 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 . . . . . . . . . .    91.30           30.3   142    94.7   150     ARMSMC  
     WELL ORDERED  . . . . .    91.30           30.3   142    94.7   150     ARMSMC  
     NO INTER CONTACTS . . .    91.30           30.3   142    94.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    90.23           32.3   130    94.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .    65.68           50.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .   101.21           22.2    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    88.76           36.8    57    91.9    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    93.82           28.6    98    92.5   106     ARMSMC  
     BURIED  . . . . . . . .    85.39           34.1    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    92.96           25.9    85    96.6    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) =   0.98356     r(1,2) =   0.16686     r(1,3) =  -0.06910 
 r(2,1) =   0.08771     r(2,2) =  -0.10688     r(2,3) =   0.99040 
 r(3,1) =   0.15787     r(3,2) =  -0.98017     r(3,3) =  -0.11976 
THE OFFSET VECTOR: 
 v(1) = -33.42126     v(2) = -81.19415     v(3) =  69.08954 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.80           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.04         73    96.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1923                            CRMSCA  
     WELL ORDERED  . . . . .   14.04         73    96.1    76     CRMSCA  
     NO INTER CONTACTS . . .   14.04         73    96.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .   13.91         67    95.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .   17.11          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   14.99         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   13.49          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   14.20         30    93.8    32     CRMSCA  
     SURFACE . . . . . . . .   14.45         51    94.4    54     CRMSCA  
     BURIED  . . . . . . . .   13.04         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .   13.93         43    97.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.93        346    93.3   371     CRMSMC  
     WELL ORDERED  . . . . .   13.93        346    93.3   371     CRMSMC  
     NO INTER CONTACTS . . .   13.93        346    93.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.76        316    92.7   341     CRMSMC  
     ALTERNATIVE PARENT  . .   16.68         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   14.97        129    97.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .   13.63         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   13.80        141    91.6   154     CRMSMC  
     SURFACE . . . . . . . .   14.33        241    91.3   264     CRMSMC  
     BURIED  . . . . . . . .   12.97        105    98.1   107     CRMSMC  
     CORE  . . . . . . . . .   14.02        205    94.5   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.77         54    19.0   284     CRMSSC  
     WELL ORDERED  . . . . .   13.77         54    19.0   284     CRMSSC  
     NO INTER CONTACTS . . .   13.77         54    19.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.77         54    22.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   15.15         21    21.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.97         21    18.8   112     CRMSSC  
     SURFACE . . . . . . . .   14.02         37    16.7   222     CRMSSC  
     BURIED  . . . . . . . .   13.19         17    27.4    62     CRMSSC  
     CORE  . . . . . . . . .   14.80         33    19.2   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.93        346    58.8   588     CRMSALL 
     WELL ORDERED  . . . . .   13.93        346    58.8   588     CRMSALL 
     NO INTER CONTACTS . . .   13.93        346    58.8   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.76        316    58.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .   16.68         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   14.97        129    62.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   13.80        141    58.8   240     CRMSALL 
     SURFACE . . . . . . . .   14.33        241    55.0   438     CRMSALL 
     BURIED  . . . . . . . .   12.97        105    70.0   150     CRMSALL 
     CORE  . . . . . . . . .   14.02        205    58.9   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    17.00      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     7.88      1    33.3     3      26-GGG-28   
 CA  LOOP  3     4.92     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    21.71      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    16.82     32    94.1    34       1-AEIEVGR-7    
 MC  LOOP  2     9.09      4    33.3    12      26-GGG-28   
 MC  LOOP  3     4.83     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    21.54     17    89.5    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    16.82     32    60.4    53       1-AEIEVGR-7    
 ALL LOOP  2     9.09      4    33.3    12      26-GGG-28   
 ALL LOOP  3     4.83     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    21.54     17    48.6    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.37      7   100.0     7       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 CA  LOOP  3     3.87     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.95      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.81     32    94.1    34       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 MC  LOOP  3     3.99     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.73     17    89.5    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.81     32    60.4    53       1-AEIEVGR-7    
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 ALL LOOP  3     3.99     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.73     17    48.6    35      65-RQGR-68   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.519      1.000       0.500     73    96.1    76     ERRCA  
     WELL ORDERED  . . . . .   12.519      1.000       0.500     73    96.1    76     ERRCA  
     NO INTER CONTACTS . . .   12.519      1.000       0.500     73    96.1    76     ERRCA  
     SHIFTED CHAIN . . . . .   12.265      1.000       0.500     67    95.7    70     ERRCA  
     ALTERNATIVE PARENT  . .   16.487      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   14.451      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   12.235      1.000       0.500     30    93.8    32     ERRCA  
     SURFACE . . . . . . . .   12.970      1.000       0.500     51    94.4    54     ERRCA  
     BURIED  . . . . . . . .   11.475      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .   12.717      1.000       0.500     43    97.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.403      1.000       0.500    346    93.3   371     ERRMC  
     WELL ORDERED  . . . . .   12.403      1.000       0.500    346    93.3   371     ERRMC  
     NO INTER CONTACTS . . .   12.403      1.000       0.500    346    93.3   371     ERRMC  
     SHIFTED CHAIN . . . . .   12.107      1.000       0.500    316    92.7   341     ERRMC  
     ALTERNATIVE PARENT  . .   16.092      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .   14.394      1.000       0.500    129    97.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   11.824      1.000       0.500    141    91.6   154     ERRMC  
     SURFACE . . . . . . . .   12.854      1.000       0.500    241    91.3   264     ERRMC  
     BURIED  . . . . . . . .   11.366      1.000       0.500    105    98.1   107     ERRMC  
     CORE  . . . . . . . . .   12.800      1.000       0.500    205    94.5   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.186      1.000       0.500     54    19.0   284     ERRSC  
     WELL ORDERED  . . . . .   12.186      1.000       0.500     54    19.0   284     ERRSC  
     NO INTER CONTACTS . . .   12.186      1.000       0.500     54    19.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .   12.186      1.000       0.500     54    22.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   11.716      1.000       0.500     48    18.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   16.422      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .   14.495      1.000       0.500     21    21.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.180      1.000       0.500     21    18.8   112     ERRSC  
     SURFACE . . . . . . . .   12.560      1.000       0.500     37    16.7   222     ERRSC  
     BURIED  . . . . . . . .   11.371      1.000       0.500     17    27.4    62     ERRSC  
     CORE  . . . . . . . . .   13.462      1.000       0.500     33    19.2   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.403      1.000       0.500    346    58.8   588     ERRALL 
     WELL ORDERED  . . . . .   12.403      1.000       0.500    346    58.8   588     ERRALL 
     NO INTER CONTACTS . . .   12.403      1.000       0.500    346    58.8   588     ERRALL 
     SHIFTED CHAIN . . . . .   12.107      1.000       0.500    316    58.3   542     ERRALL 
     ALTERNATIVE PARENT  . .   16.092      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .   14.394      1.000       0.500    129    62.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   11.824      1.000       0.500    141    58.8   240     ERRALL 
     SURFACE . . . . . . . .   12.854      1.000       0.500    241    55.0   438     ERRALL 
     BURIED  . . . . . . . .   11.366      1.000       0.500    105    70.0   150     ERRALL 
     CORE  . . . . . . . . .   12.800      1.000       0.500    205    58.9   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)         2         4         8        13        25      73      76   DISTCA 
CA  (P)      2.63      5.26     10.53     17.11     32.89              76   DISTCA 
CA  (RMS)    0.74      1.17      1.80      2.87      6.14                   DISTCA 
 
ALL (N)         5        22        36        66       124     346     588   DISTALL 
ALL (P)      0.85      3.74      6.12     11.22     21.09             588   DISTALL 
ALL (RMS)    0.83      1.28      1.84      3.04      6.17                   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            43            30          RMSLSI 
CA  (P)       57.89         56.58         39.47          RMSLSI 
CA  (RMS)      1.67         13.93         14.20          RMSLSI 
 
 
 
END of the results output 
