 
####################################################### 
#                                                     # 
#                        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 489 atoms, 432 common with TARGET 
           Number of atoms possible to evaluate: 248 
 
 
 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 . . . . . . . . . .    91.50           24.4    86    57.3   150     ARMSMC  
     WELL ORDERED  . . . . .    91.50           24.4    86    57.3   150     ARMSMC  
     NO INTER CONTACTS . . .    91.50           24.4    86    57.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    91.99           24.7    81    58.7   138     ARMSMC  
     ALTERNATIVE PARENT  . .    86.90           12.5     8    80.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    98.27           20.6    34    63.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS   105.59           13.2    38    61.3    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    90.11           27.1    59    55.7   106     ARMSMC  
     BURIED  . . . . . . . .    94.45           18.5    27    61.4    44     ARMSMC  
     CORE  . . . . . . . . .    78.56           33.3    48    54.5    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) =   0.11820     r(1,2) =   0.98683     r(1,3) =  -0.11043 
 r(2,1) =   0.55383     r(2,2) =   0.02679     r(2,3) =   0.83220 
 r(3,1) =   0.82419     r(3,2) =  -0.15953     r(3,3) =  -0.54337 
THE OFFSET VECTOR: 
 v(1) = -16.98147     v(2) = -15.58036     v(3) =  -2.01712 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.49           (Number of atoms:    5) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.21         51    67.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2786                            CRMSCA  
     WELL ORDERED  . . . . .   14.21         51    67.1    76     CRMSCA  
     NO INTER CONTACTS . . .   14.21         51    67.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.62         47    67.1    70     CRMSCA  
     ALTERNATIVE PARENT  . .   13.85          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   13.42         20    74.1    27     CRMSCA  
     SHIFTED SS UNITS  . . .   13.46          3    50.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.25         22    68.8    32     CRMSCA  
     SURFACE . . . . . . . .   14.93         36    66.7    54     CRMSCA  
     BURIED  . . . . . . . .   12.32         15    68.2    22     CRMSCA  
     CORE  . . . . . . . . .   12.44         29    65.9    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.36        248    66.8   371     CRMSMC  
     WELL ORDERED  . . . . .   14.36        248    66.8   371     CRMSMC  
     NO INTER CONTACTS . . .   14.36        248    66.8   371     CRMSMC  
     SHIFTED CHAIN . . . . .   14.79        228    66.9   341     CRMSMC  
     ALTERNATIVE PARENT  . .   13.85         19    76.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   13.52         98    73.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .   13.55         15    50.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   16.56        105    68.2   154     CRMSMC  
     SURFACE . . . . . . . .   15.06        175    66.3   264     CRMSMC  
     BURIED  . . . . . . . .   12.51         73    68.2   107     CRMSMC  
     CORE  . . . . . . . . .   12.50        143    65.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   15.24         44    15.5   284     CRMSSC  
     WELL ORDERED  . . . . .   15.24         44    15.5   284     CRMSSC  
     NO INTER CONTACTS . . .   15.24         44    15.5   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   15.24         44    18.3   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   14.10         18    18.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   18.06         17    15.2   112     CRMSSC  
     SURFACE . . . . . . . .   15.90         31    14.0   222     CRMSSC  
     BURIED  . . . . . . . .   13.53         13    21.0    62     CRMSSC  
     CORE  . . . . . . . . .   13.15         27    15.7   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.36        248    42.2   588     CRMSALL 
     WELL ORDERED  . . . . .   14.36        248    42.2   588     CRMSALL 
     NO INTER CONTACTS . . .   14.36        248    42.2   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.79        228    42.1   542     CRMSALL 
     ALTERNATIVE PARENT  . .   13.85         19    42.2    45     CRMSALL 
     SECONDARY STRUCTURE . .   13.52         98    47.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   16.56        105    43.8   240     CRMSALL 
     SURFACE . . . . . . . .   15.06        175    40.0   438     CRMSALL 
     BURIED  . . . . . . . .   12.51         73    48.7   150     CRMSALL 
     CORE  . . . . . . . . .   12.50        143    41.1   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    31.10      3    42.9     7       1-AEIEVGR-7    
 CA  LOOP  2     2.88      3   100.0     3      26-GGG-28   
 CA  LOOP  3    15.84      5    50.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    13.73      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    31.22     15    44.1    34       1-AEIEVGR-7    
 MC  LOOP  2     3.02     12   100.0    12      26-GGG-28   
 MC  LOOP  3    15.60     25    50.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    13.59     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    31.22     15    28.3    53       1-AEIEVGR-7    
 ALL LOOP  2     3.02     12   100.0    12      26-GGG-28   
 ALL LOOP  3    15.60     25    28.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    13.59     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.15      3    42.9     7       1-AEIEVGR-7    
 CA  LOOP  2     0.10      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.04      5    50.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.11      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.05     15    44.1    34       1-AEIEVGR-7    
 MC  LOOP  2     1.80     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.38     25    50.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.36     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.05     15    28.3    53       1-AEIEVGR-7    
 ALL LOOP  2     1.80     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.38     25    28.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.36     18    51.4    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 . . . . . . . . . .   12.106      1.000       0.500     51    67.1    76     ERRCA  
     WELL ORDERED  . . . . .   12.106      1.000       0.500     51    67.1    76     ERRCA  
     NO INTER CONTACTS . . .   12.106      1.000       0.500     51    67.1    76     ERRCA  
     SHIFTED CHAIN . . . . .   12.548      1.000       0.500     47    67.1    70     ERRCA  
     ALTERNATIVE PARENT  . .   13.716      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .   11.548      1.000       0.500     20    74.1    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   14.065      1.000       0.500     22    68.8    32     ERRCA  
     SURFACE . . . . . . . .   12.646      1.000       0.500     36    66.7    54     ERRCA  
     BURIED  . . . . . . . .   10.811      1.000       0.500     15    68.2    22     ERRCA  
     CORE  . . . . . . . . .   10.620      1.000       0.500     29    65.9    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.343      1.000       0.500    248    66.8   371     ERRMC  
     WELL ORDERED  . . . . .   12.343      1.000       0.500    248    66.8   371     ERRMC  
     NO INTER CONTACTS . . .   12.343      1.000       0.500    248    66.8   371     ERRMC  
     SHIFTED CHAIN . . . . .   12.791      1.000       0.500    228    66.9   341     ERRMC  
     ALTERNATIVE PARENT  . .   13.718      1.000       0.500     19    76.0    25     ERRMC  
     SECONDARY STRUCTURE . .   11.758      1.000       0.500     98    73.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   14.464      1.000       0.500    105    68.2   154     ERRMC  
     SURFACE . . . . . . . .   12.847      1.000       0.500    175    66.3   264     ERRMC  
     BURIED  . . . . . . . .   11.134      1.000       0.500     73    68.2   107     ERRMC  
     CORE  . . . . . . . . .   10.785      1.000       0.500    143    65.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.452      1.000       0.500     44    15.5   284     ERRSC  
     WELL ORDERED  . . . . .   13.452      1.000       0.500     44    15.5   284     ERRSC  
     NO INTER CONTACTS . . .   13.452      1.000       0.500     44    15.5   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.452      1.000       0.500     44    18.3   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   14.088      1.000       0.500     40    15.3   262     ERRSC  
     ALTERNATIVE PARENT  . .   13.774      1.000       0.500      3    12.0    25     ERRSC  
     SECONDARY STRUCTURE . .   12.409      1.000       0.500     18    18.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   16.411      1.000       0.500     17    15.2   112     ERRSC  
     SURFACE . . . . . . . .   14.020      1.000       0.500     31    14.0   222     ERRSC  
     BURIED  . . . . . . . .   12.097      1.000       0.500     13    21.0    62     ERRSC  
     CORE  . . . . . . . . .   11.589      1.000       0.500     27    15.7   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.343      1.000       0.500    248    42.2   588     ERRALL 
     WELL ORDERED  . . . . .   12.343      1.000       0.500    248    42.2   588     ERRALL 
     NO INTER CONTACTS . . .   12.343      1.000       0.500    248    42.2   588     ERRALL 
     SHIFTED CHAIN . . . . .   12.791      1.000       0.500    228    42.1   542     ERRALL 
     ALTERNATIVE PARENT  . .   13.718      1.000       0.500     19    42.2    45     ERRALL 
     SECONDARY STRUCTURE . .   11.758      1.000       0.500     98    47.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   14.464      1.000       0.500    105    43.8   240     ERRALL 
     SURFACE . . . . . . . .   12.847      1.000       0.500    175    40.0   438     ERRALL 
     BURIED  . . . . . . . .   11.134      1.000       0.500     73    48.7   150     ERRALL 
     CORE  . . . . . . . . .   10.785      1.000       0.500    143    41.1   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         5         5         9        21      51      76   DISTCA 
CA  (P)      1.32      6.58      6.58     11.84     27.63              76   DISTCA 
CA  (RMS)    0.77      1.49      1.49      3.10      6.50                   DISTCA 
 
ALL (N)         1        11        18        42        96     248     588   DISTALL 
ALL (P)      0.17      1.87      3.06      7.14     16.33             588   DISTALL 
ALL (RMS)    0.77      1.62      2.02      3.31      6.39                   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            29            22          RMSLSI 
CA  (P)       57.89         38.16         28.95          RMSLSI 
CA  (RMS)      1.67         12.44         16.25          RMSLSI 
 
 
 
END of the results output 
