
 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)@comp33.ch.
                 Created on  5/28/12 at 12:34:24 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=    -378.2543928     RMS force=    0.9482239899E-06
 OPTIM> Final energy  =    -382.1851430     RMS force=    0.9692575181E-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=     43885.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.27     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.168613344    
 Double-ended search iterations= 350 RMS= 0.2348 Dev= 2.06% S= 42.21 time= 3.83
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         92
 DNEB run yielded 2 true transition state(s) time=  13.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1002 steps. Energy=    -378.2543928       time=       3.00
 Minus side of path:                    1053 steps. Energy=    -380.8184152       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.2543928  2.3854         -375.8690199  4.9494         -380.8184152  18.192  14.724  13.156  11.022
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1062 steps. Energy=    -380.7727545       time=       3.56
 Minus side of path:                    1079 steps. Energy=    -380.8184152       time=       4.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545  1.3782         -379.3945995  1.4238         -380.8184152  34.422  32.218   3.277  44.248
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1101.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.33     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 0.7729 Dev= 0.94% S= 14.67 time= 0.37
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  43.14
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2203.5    
 decide> The unconnected minima in the chain and their distances are:
     2       10.33     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 805 RMS= 0.0251 Dev= 5.26% S= 20.74 time= 20.39
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         98
 DNEB run yielded 1 true transition state(s) time=   8.84

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     961 steps. Energy=    -382.1851430       time=       3.24
 Minus side of path:                     963 steps. Energy=    -382.2275456       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1851430 0.20661E-01     -382.1644819 0.63064E-01     -382.2275456   1.100   1.089  15.621   9.282
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1176.9    
 decide> The unconnected minima in the chain and their distances are:
     5       10.56     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 105 RMS= 0.7205 Dev= 2.85% S= 14.97 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   7.80

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     986 steps. Energy=    -380.7879935       time=       2.97
 Minus side of path:                    1009 steps. Energy=    -380.7727545       time=       3.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7879935 0.25640E-01     -380.7623536 0.10401E-01     -380.7727545   1.577   1.574   2.911  49.815
        *NEW* (Placed in 6)                                     Known (#4)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1124.5    
 decide> The unconnected minima in the chain and their distances are:
     2       10.40     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 105 RMS= 1.6124 Dev= 2.53% S= 14.75 time= 0.37
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   4.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1035 steps. Energy=    -380.7879935       time=       3.26
 Minus side of path:                    1012 steps. Energy=    -382.1663989       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7879935  2.3717         -378.4162786  3.7501         -382.1663989  18.723  10.388  22.693   6.390
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     5.2721    
 decide> The unconnected minima in the chain and their distances are:
     2        1.74     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0142 Dev= 0.03% S= 1.74 time= 0.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.66

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1014 steps. Energy=    -382.1851430       time=       3.05
 Minus side of path:                    1002 steps. Energy=    -382.1663989       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1851430 0.33047E-01     -382.1520962 0.14303E-01     -382.1663989   1.745   1.740   2.843  51.010
        Known (#2)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -378.2543928  2.3854        -375.8690199  4.9494        -380.8184152  18.192  14.724  13.156  11.022
   2     -380.8184152  1.4238        -379.3945995  1.3782        -380.7727545  34.422  32.218   3.277  44.248
   4     -380.7727545 0.10401E-01    -380.7623536 0.25640E-01    -380.7879935   1.577   1.574   2.911  49.815
   5     -380.7879935  2.3717        -378.4162786  3.7501        -382.1663989  18.723  10.388  22.693   6.390
   6     -382.1663989 0.14303E-01    -382.1520962 0.33047E-01    -382.1851430   1.745   1.740   2.843  51.010

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               145.76
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45099 time=          48.17 %= 33.1
 OPTIM> # of energy+gradient+Hessian calls=       634 time=           2.78 %=  1.9
