
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> Number of atoms (or variables)  determined as    145
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp25.ch.
                 Created on  5/28/12 at 13: 4:50 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  435 Cartesian coordinates will be optimised for  145 CHARMM atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -380.8338166     RMS force=    0.9354595595E-06
 OPTIM> Final energy  =    -383.4321120     RMS force=    0.8919538587E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     59594.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.06     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      41.16135595    
 Double-ended search iterations= 385 RMS= 2.6745 Dev= 0.62% S= 40.44 time= 4.89
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  14.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1048 steps. Energy=    -380.1974415       time=       3.70
 Minus side of path:                    1192 steps. Energy=    -380.8223643       time=       3.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1974415 0.35057         -379.8468681 0.97550         -380.8223643  37.722  36.687   2.351  61.665
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     59472.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.03     4     4        0.96     1 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 4_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 385 RMS= 0.1225 Dev= 0.44% S= 40.68 time= 4.95
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        216
 DNEB run yielded 1 true transition state(s) time=  30.58

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1254 steps. Energy=    -380.7514154       time=       5.56
 Minus side of path:                    1507 steps. Energy=    -380.8223643       time=       6.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7514154 0.88919         -379.8622210 0.96014         -380.8223643  47.463  44.210   1.968  73.684
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0136 Dev= 0.72% S= 0.97 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.96

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     962 steps. Energy=    -380.8338166       time=       3.31
 Minus side of path:                     985 steps. Energy=    -380.8223643       time=       3.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.8338166 0.44962E-01     -380.7888541 0.33510E-01     -380.8223643   0.978   0.964  30.390   4.771
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     69149.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.05     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_S using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      227.0466720    
 Double-ended search iterations= 420 RMS= 1.2538 Dev= 1.11% S= 42.54 time= 6.18
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=  14.47

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     983 steps. Energy=    -380.8223643       time=       3.84
 Minus side of path:                     959 steps. Energy=    -380.7263586       time=       3.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.8223643 0.11172         -380.7106430 0.15716E-01     -380.7263586   1.035   1.033  40.443   3.585
        Known (#4)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     58997.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.93     6 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 6_S using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 385 RMS= 0.6662 Dev= 0.98% S= 40.59 time= 4.87
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   7.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1047 steps. Energy=    -382.0963772       time=       3.20
 Minus side of path:                    1019 steps. Energy=    -380.8629455       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0963772  4.2116         -377.8847313  2.9782         -380.8629455  18.423  10.963  15.209   9.534
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     54467.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.90     7     8        2.26     4 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 7_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 385 RMS= 0.0473 Dev= 0.18% S= 38.25 time= 4.84
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        142
 DNEB run yielded 1 true transition state(s) time=  18.62

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1085 steps. Energy=    -382.0963772       time=       3.59
 Minus side of path:                    1023 steps. Energy=    -380.7633954       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0963772  1.3581         -380.7382567 0.25139E-01     -380.7633954  27.714  27.052   2.238  64.784
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0139 Dev= 0.22% S= 2.26 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.47

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1011 steps. Energy=    -380.8223643       time=       2.91
 Minus side of path:                    1001 steps. Energy=    -380.8629455       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.8223643 0.18849E-01     -380.8035154 0.59430E-01     -380.8629455   2.278   2.259   3.631  39.934
        Known (#4)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     10203.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.69     9 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 9_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 210 RMS= 0.1518 Dev= 0.33% S= 21.79 time= 1.56
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.83

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     998 steps. Energy=    -380.7633954       time=       3.76
 Minus side of path:                    1066 steps. Energy=    -383.4302015       time=       4.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7633954 0.34114E-01     -380.7292816  2.7009         -383.4302015  21.164  21.003   1.782  81.367
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3.7946    
 decide> The unconnected minima in the chain and their distances are:
     2        1.56    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0162 Dev= 0.53% S= 1.56 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   4.28

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     982 steps. Energy=    -383.4321120       time=       4.13
 Minus side of path:                     979 steps. Energy=    -383.4302015       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4321120 0.67719E-01     -383.3643932 0.65808E-01     -383.4302015   1.572   1.560   3.855  37.609
        Known (#2)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -380.8338166 0.44962E-01    -380.7888541 0.33510E-01    -380.8223643   0.978   0.964  30.390   4.771
   7     -380.8223643 0.18849E-01    -380.8035154 0.59430E-01    -380.8629455   2.278   2.259   3.631  39.934
   5     -380.8629455  2.9782        -377.8847313  4.2116        -382.0963772  18.423  10.963  15.209   9.534
   6     -382.0963772  1.3581        -380.7382567 0.25139E-01    -380.7633954  27.714  27.052   2.238  64.784
   8     -380.7633954 0.34114E-01    -380.7292816  2.7009        -383.4302015  21.164  21.003   1.782  81.367
   9     -383.4302015 0.65808E-01    -383.3643932 0.67719E-01    -383.4321120   1.572   1.560   3.855  37.609

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               197.21
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             55471 time=          63.43 %= 32.2
 OPTIM> # of energy+gradient+Hessian calls=       677 time=           3.44 %=  1.7
