
 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)@comp34.ch.
                 Created on  5/28/12 at 13: 5:26 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=    -390.2596686     RMS force=    0.9377387882E-06
 OPTIM> Final energy  =    -389.0755876     RMS force=    0.9194710027E-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=     14826.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.57     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 245 RMS= 0.4528 Dev= 0.98% S= 25.05 time= 2.38
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   7.03

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     982 steps. Energy=    -390.5076396       time=       2.64
 Minus side of path:                     953 steps. Energy=    -389.9883114       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5076396  1.4275         -389.0801577 0.90815         -389.9883114  16.854   7.091   3.938  36.823
        *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      3 steps with      2 missing connections, weight=     8595.3    
 decide> The unconnected minima in the chain and their distances are:
     2       19.56     3     4       10.35     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 175 RMS= 0.6248 Dev= 0.76% S= 19.86 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.57

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1046 steps. Energy=    -389.0755876       time=       3.59
 Minus side of path:                     998 steps. Energy=    -390.5076396       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0755876  2.8789         -386.1966615  4.3110         -390.5076396  23.524  19.565   2.957  49.032
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 0.2127 Dev= 0.64% S= 10.39 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.63

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     979 steps. Energy=    -390.2108175       time=       2.69
 Minus side of path:                     962 steps. Energy=    -389.9883114       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2108175  2.1780         -388.0328634  1.9554         -389.9883114  11.808  10.609   2.579  56.228
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     34.170    
 decide> The unconnected minima in the chain and their distances are:
     5        3.25     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0480 Dev= 0.45% S= 3.30 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.07

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     906 steps. Energy=    -390.2108175       time=       3.04
 Minus side of path:                     929 steps. Energy=    -390.2596686       time=       3.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2108175 0.65246E-02     -390.2042929 0.55376E-01     -390.2596686   3.306   3.245  33.751   4.296
        Known (#5)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -390.2596686 0.55376E-01    -390.2042929 0.65246E-02    -390.2108175   3.306   3.245  33.751   4.296
   3     -390.2108175  2.1780        -388.0328634  1.9554        -389.9883114  11.808  10.609   2.579  56.228
   1     -389.9883114 0.90815        -389.0801577  1.4275        -390.5076396  16.854   7.091   3.938  36.823
   2     -390.5076396  4.3110        -386.1966615  2.8789        -389.0755876  23.524  19.565   2.957  49.032

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

 Elapsed time=                                50.11
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             14792 time=          20.26 %= 40.4
 OPTIM> # of energy+gradient+Hessian calls=       170 time=           0.82 %=  1.6
