
 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)@comp23.ch.
                 Created on  5/28/12 at 12:42:56 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=    -381.2087228     RMS force=    0.9379963411E-06
 OPTIM> Final energy  =    -386.1359640     RMS force=    0.9979167905E-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=     46666.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.00     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 350 RMS= 0.0843 Dev= 1.90% S= 41.72 time= 4.11
 Following    2 images are candidates for TS:    1    6  
 Converged to TS (number of iterations):         54
 Converged to TS (number of iterations):         76
 DNEB run yielded 2 true transition state(s) time=  12.24

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     985 steps. Energy=    -381.3101755       time=       2.97
 Minus side of path:                    1020 steps. Energy=    -385.4109265       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3101755 0.79286E-01     -381.2308898  4.1800         -385.4109265  14.426  12.291   7.598  19.084
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1070 steps. Energy=    -386.1359640       time=       4.11
 Minus side of path:                    1061 steps. Energy=    -385.3045545       time=       3.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1359640  1.8230         -384.3129228 0.99163         -385.3045545  39.431  36.406   3.609  40.182
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     224.01    
 decide> The unconnected minima in the chain and their distances are:
     5        6.06     4     3        1.10     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.4394 Dev= 0.69% S= 6.61 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   9.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1007 steps. Energy=    -385.4109265       time=       3.58
 Minus side of path:                    1072 steps. Energy=    -387.4639584       time=       3.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4109265 0.30359         -385.1073348  2.3566         -387.4639584  45.908  43.246   2.204  65.776
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2059 Dev= 0.27% S= 1.11 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     977 steps. Energy=    -381.3101755       time=       2.49
 Minus side of path:                     998 steps. Energy=    -381.2087228       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3101755 0.11624         -381.1939334 0.14789E-01     -381.2087228   1.128   1.102   7.294  19.880
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     445.34    
 decide> The unconnected minima in the chain and their distances are:
     5        6.06     4 
 

 tryconnect> 455-iteration DNEB run for minima 4_S and 5_F using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 455 RMS= 0.0241 Dev= 3.62% S= 8.88 time= 7.11
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.98

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1018 steps. Energy=    -385.3045545       time=       2.43
 Minus side of path:                    1007 steps. Energy=    -385.4109265       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3045545  2.8094         -382.4951299  2.9158         -385.4109265   7.073   6.062  25.453   5.697
        Known (#5)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -381.2087228 0.14789E-01    -381.1939334 0.11624        -381.3101755   1.128   1.102   7.294  19.880
   1     -381.3101755 0.79286E-01    -381.2308898  4.1800        -385.4109265  14.426  12.291   7.598  19.084
   5     -385.4109265  2.9158        -382.4951299  2.8094        -385.3045545   7.073   6.062  25.453   5.697
   2     -385.3045545 0.99163        -384.3129228  1.8230        -386.1359640  39.431  36.406   3.609  40.182

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                72.31
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             25227 time=          29.28 %= 40.5
 OPTIM> # of energy+gradient+Hessian calls=       240 time=           1.02 %=  1.4
