 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0047.inter 
# 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0047.1mup.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0047.1obp_A.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0047.1beb_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0047.1epa_B.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 1287 atoms, MODEL 672 atoms, 656 common with TARGET 
           Number of atoms possible to evaluate: 562 
 
 
 CA-RMS TARGET<->PARENT(1mup)	 1.202822 
 
 CA-RMS TARGET<->PARENT(1obp-A)	 2.128074 
 
 CA-RMS TARGET<->PARENT(1beb-A)	 2.195152 
 
 CA-RMS TARGET<->PARENT(1epa-B)	 1.899896 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.03           61.5   270    86.0   314     ARMSMC  
     WELL ORDERED  . . . . .    65.00           57.6   184    96.8   190     ARMSMC  
     NO INTER CONTACTS . . .    60.55           63.2   250    85.0   294     ARMSMC  
     SHIFTED CHAIN . . . . .    83.19           46.2    52    82.5    63     ARMSMC  
     ALTERNATIVE PARENT  . .    86.43           42.9    14   100.0    14     ARMSMC  
     SECONDARY STRUCTURE . .    43.94           75.8   153    94.4   162     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.76           36.4    22   100.0    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    62.72           64.4   132    80.5   164     ARMSMC  
     BURIED  . . . . . . . .    65.26           58.7   138    92.0   150     ARMSMC  
     CORE  . . . . . . . . .    63.20           63.7   248    84.9   292     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   141     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    59     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   131     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   132     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    65     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    28     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    75     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     9     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    77     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    64     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   132     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   111     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   103     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    84     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    64     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    20     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    59     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     7     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    64     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   104     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    43     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     7     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    38     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    41     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    35     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     3     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    20     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    22     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     4     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    18     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    22     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    19     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    10     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    19     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.69279     r(1,2) =  -0.58425     r(1,3) =   0.42273 
 r(2,1) =  -0.71270     r(2,2) =  -0.64413     r(2,3) =   0.27776 
 r(3,1) =   0.11002     r(3,2) =  -0.49371     r(3,3) =  -0.86264 
THE OFFSET VECTOR: 
 v(1) =  63.19171     v(2) =   9.20358     v(3) =  66.59100 
 
 Number of iteration 50                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.20           (Number of atoms:   56) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.86        145    91.8   158     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0266                            CRMSCA  
     WELL ORDERED  . . . . .    4.05         94    98.9    95     CRMSCA  
     NO INTER CONTACTS . . .    3.82        135    91.2   148     CRMSCA  
     SHIFTED CHAIN . . . . .    3.75         28    87.5    32     CRMSCA  
     ALTERNATIVE PARENT  . .    3.21          7   100.0     7     CRMSCA  
     SECONDARY STRUCTURE . .    2.72         78    96.3    81     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.66         11   100.0    11     CRMSCA  
     SURFACE . . . . . . . .    3.86         72    86.7    83     CRMSCA  
     BURIED  . . . . . . . .    3.86         73    97.3    75     CRMSCA  
     CORE  . . . . . . . . .    3.88        134    91.2   147     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.78        562    72.1   779     CRMSMC  
     WELL ORDERED  . . . . .    4.02        376    83.0   453     CRMSMC  
     NO INTER CONTACTS . . .    3.73        522    71.6   729     CRMSMC  
     SHIFTED CHAIN . . . . .    3.66        109    69.9   156     CRMSMC  
     ALTERNATIVE PARENT  . .    3.24         28    84.8    33     CRMSMC  
     SECONDARY STRUCTURE . .    2.78        312    77.6   402     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.65         44    83.0    53     CRMSMC  
     SURFACE . . . . . . . .    3.71        276    67.2   411     CRMSMC  
     BURIED  . . . . . . . .    3.85        286    77.7   368     CRMSMC  
     CORE  . . . . . . . . .    3.80        518    71.3   726     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   655     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   321     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   606     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   573     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   307     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   357     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    42     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   360     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   295     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   613     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.78        562    43.7  1287     CRMSALL 
     WELL ORDERED  . . . . .    4.02        376    53.6   701     CRMSALL 
     NO INTER CONTACTS . . .    3.73        522    43.6  1198     CRMSALL 
     SHIFTED CHAIN . . . . .    3.66        109    44.3   246     CRMSALL 
     ALTERNATIVE PARENT  . .    3.24         28    54.9    51     CRMSALL 
     SECONDARY STRUCTURE . .    2.78        312    45.8   681     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.65         44    51.2    86     CRMSALL 
     SURFACE . . . . . . . .    3.71        276    39.9   692     CRMSALL 
     BURIED  . . . . . . . .    3.85        286    48.1   595     CRMSALL 
     CORE  . . . . . . . . .    3.80        518    43.1  1201     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.94      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     4.61      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.88     16    84.2    19      60-ENGE-63   
 MC  LOOP  2     4.51     20    80.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.88     16    53.3    30      60-ENGE-63   
 ALL LOOP  2     4.51     20    48.8    41     153-KTDRC-157  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.03      4   100.0     4      60-ENGE-63   
 CA  LOOP  2     1.64      5   100.0     5     153-KTDRC-157  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.16     16    84.2    19      60-ENGE-63   
 MC  LOOP  2     1.65     20    80.0    25     153-KTDRC-157  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.16     16    53.3    30      60-ENGE-63   
 ALL LOOP  2     1.65     20    48.8    41     153-KTDRC-157  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.152      1.000       0.500    145    91.8   158     ERRCA  
     WELL ORDERED  . . . . .    3.304      1.000       0.500     94    98.9    95     ERRCA  
     NO INTER CONTACTS . . .    3.075      1.000       0.500    135    91.2   148     ERRCA  
     SHIFTED CHAIN . . . . .    3.413      1.000       0.500     28    87.5    32     ERRCA  
     ALTERNATIVE PARENT  . .    2.860      1.000       0.500      7   100.0     7     ERRCA  
     SECONDARY STRUCTURE . .    2.314      1.000       0.500     78    96.3    81     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.276      1.000       0.500     11   100.0    11     ERRCA  
     SURFACE . . . . . . . .    3.055      1.000       0.500     72    86.7    83     ERRCA  
     BURIED  . . . . . . . .    3.246      1.000       0.500     73    97.3    75     ERRCA  
     CORE  . . . . . . . . .    3.141      1.000       0.500    134    91.2   147     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.079      1.000       0.500    562    72.1   779     ERRMC  
     WELL ORDERED  . . . . .    3.312      1.000       0.500    376    83.0   453     ERRMC  
     NO INTER CONTACTS . . .    2.992      1.000       0.500    522    71.6   729     ERRMC  
     SHIFTED CHAIN . . . . .    3.280      1.000       0.500    109    69.9   156     ERRMC  
     ALTERNATIVE PARENT  . .    2.805      1.000       0.500     28    84.8    33     ERRMC  
     SECONDARY STRUCTURE . .    2.352      1.000       0.500    312    77.6   402     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.241      1.000       0.500     44    83.0    53     ERRMC  
     SURFACE . . . . . . . .    2.921      1.000       0.500    276    67.2   411     ERRMC  
     BURIED  . . . . . . . .    3.233      1.000       0.500    286    77.7   368     ERRMC  
     CORE  . . . . . . . . .    3.066      1.000       0.500    518    71.3   726     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   655     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   321     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   606     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   573     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   307     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   118     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    23     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   357     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    42     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   360     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   295     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   613     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.079      1.000       0.500    562    43.7  1287     ERRALL 
     WELL ORDERED  . . . . .    3.312      1.000       0.500    376    53.6   701     ERRALL 
     NO INTER CONTACTS . . .    2.992      1.000       0.500    522    43.6  1198     ERRALL 
     SHIFTED CHAIN . . . . .    3.280      1.000       0.500    109    44.3   246     ERRALL 
     ALTERNATIVE PARENT  . .    2.805      1.000       0.500     28    54.9    51     ERRALL 
     SECONDARY STRUCTURE . .    2.352      1.000       0.500    312    45.8   681     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.241      1.000       0.500     44    51.2    86     ERRALL 
     SURFACE . . . . . . . .    2.921      1.000       0.500    276    39.9   692     ERRALL 
     BURIED  . . . . . . . .    3.233      1.000       0.500    286    48.1   595     ERRALL 
     CORE  . . . . . . . . .    3.066      1.000       0.500    518    43.1  1201     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)        31        53        62       128       143     145     158   DISTCA 
CA  (P)     19.62     33.54     39.24     81.01     90.51             158   DISTCA 
CA  (RMS)    0.69      1.12      1.44      3.01      3.51                   DISTCA 
 
ALL (N)       119       203       258       494       553     562    1287   DISTALL 
ALL (P)      9.25     15.77     20.05     38.38     42.97            1287   DISTALL 
ALL (RMS)    0.68      1.08      1.53      2.93      3.42                   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)         147           134            11          RMSLSI 
CA  (P)       93.04         84.81          6.96          RMSLSI 
CA  (RMS)      0.77          3.88          3.66          RMSLSI 
 
 
 
END of the results output 
