
 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)@comp26.ch.
                 Created on  5/28/12 at 12:48:59 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=    -388.8174209     RMS force=    0.9142892131E-06
 OPTIM> Final energy  =    -385.4791588     RMS force=    0.9033076212E-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=     11171.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.35     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1531 Dev= 0.94% S= 23.10 time= 1.69
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        143
 DNEB run yielded 1 true transition state(s) time=  13.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     957 steps. Energy=    -386.9948355       time=       2.72
 Minus side of path:                    1134 steps. Energy=    -394.6417674       time=       3.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9948355 0.14120         -386.8536333  7.7881         -394.6417674  23.017  21.846   2.385  60.787
        *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      1 steps with      1 missing connections, weight=     22341.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.35     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 805 RMS= 0.0397 Dev= 6.39% S= 30.86 time= 24.56
 Following    3 images are candidates for TS:   13   18   22  
 Converged to TS (number of iterations):        116
 Converged to TS (number of iterations):        103
 Converged to TS (number of iterations):         93
 DNEB run yielded 3 true transition state(s) time=  36.43

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     961 steps. Energy=    -391.6351044       time=       2.40
 Minus side of path:                     928 steps. Energy=    -394.6417674       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6351044  1.1367         -390.4984037  4.1434         -394.6417674   7.037   6.200  14.243  10.180
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     907 steps. Energy=    -385.4791588       time=       2.05
 Minus side of path:                     969 steps. Energy=    -385.8162135       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4791588 0.22210E-01     -385.4569492 0.35926         -385.8162135   9.369   9.188   6.202  23.379
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1057 steps. Energy=    -385.8162135       time=       3.52
 Minus side of path:                     930 steps. Energy=    -385.3038899       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8162135 0.53146         -385.2847545 0.19135E-01     -385.3038899  15.185  14.839   3.351  43.273
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6977.6    
 decide> The unconnected minima in the chain and their distances are:
     7       19.11     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 7_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 175 RMS= 0.0866 Dev= 0.94% S= 19.56 time= 1.11
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.99

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1057 steps. Energy=    -388.8174209       time=       2.59
 Minus side of path:                     959 steps. Energy=    -385.5722824       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.8174209  4.7865         -384.0309336  1.5413         -385.5722824  18.710  17.975   2.712  53.476
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     71.569    
 decide> The unconnected minima in the chain and their distances are:
     7        4.15     8 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0414 Dev= 0.53% S= 4.16 time= 0.18
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   5.72

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     967 steps. Energy=    -385.5722824       time=       3.91
 Minus side of path:                     948 steps. Energy=    -385.3038899       time=       4.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5722824 0.27556         -385.2967190 0.71708E-02     -385.3038899   4.182   4.152   3.578  40.524
        Known (#8)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -388.8174209  4.7865        -384.0309336  1.5413        -385.5722824  18.710  17.975   2.712  53.476
   6     -385.5722824 0.27556        -385.2967190 0.71708E-02    -385.3038899   4.182   4.152   3.578  40.524
   4     -385.3038899 0.19135E-01    -385.2847545 0.53146        -385.8162135  15.185  14.839   3.351  43.273
   3     -385.8162135 0.35926        -385.4569492 0.22210E-01    -385.4791588   9.369   9.188   6.202  23.379

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

 Elapsed time=                               122.83
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39316 time=          50.01 %= 40.7
 OPTIM> # of energy+gradient+Hessian calls=       516 time=           2.80 %=  2.3
