
 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)@comp24.ch.
                 Created on  5/28/12 at 13: 6: 8 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=    -380.0677513     RMS force=    0.9921181688E-06
 OPTIM> Final energy  =    -385.0052262     RMS force=    0.9812633651E-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=     40714.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.40     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      70.39988712    
 Double-ended search iterations= 350 RMS= 0.4732 Dev= 0.76% S= 34.98 time= 4.91
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=   9.94

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1073 steps. Energy=    -390.4847275       time=       3.97
 Minus side of path:                     934 steps. Energy=    -385.0052262       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4847275  5.5354         -384.9492931 0.55933E-01     -385.0052262  17.098  15.500   5.113  28.361
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     18200.    
 decide> The unconnected minima in the chain and their distances are:
     3       26.30     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 245 RMS= 0.7220 Dev= 0.36% S= 26.75 time= 2.42
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   7.44

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     880 steps. Energy=    -388.6659386       time=       3.10
 Minus side of path:                     880 steps. Energy=    -390.4847275       time=       3.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6659386  2.0329         -386.6330395  3.8517         -390.4847275   6.906   6.726   5.146  28.177
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     15379.    
 decide> The unconnected minima in the chain and their distances are:
     4       24.87     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 245 RMS= 0.3514 Dev= 0.46% S= 25.44 time= 2.40
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.51

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     919 steps. Energy=    -388.6659386       time=       2.86
 Minus side of path:                     898 steps. Energy=    -391.1766914       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6659386  2.6151         -386.0508087  5.1259         -391.1766914  10.039   9.083   8.096  17.909
        Known (#4)                                              *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=     25176.    
 decide> The unconnected minima in the chain and their distances are:
     5       29.31     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 5_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      35.55672688    
 Double-ended search iterations= 280 RMS= 0.3558 Dev= 0.37% S= 29.51 time= 3.07
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=   7.97

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1259 steps. Energy=    -391.1766914       time=       4.53
 Minus side of path:                     927 steps. Energy=    -380.1019042       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1766914  11.083         -380.0937340 0.81702E-02     -380.1019042  24.118  23.693   2.542  57.050
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     371.15    
 decide> The unconnected minima in the chain and their distances are:
     6        7.19     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0404 Dev= 0.13% S= 7.19 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     950 steps. Energy=    -380.1019042       time=       2.84
 Minus side of path:                     905 steps. Energy=    -380.0677513       time=       1.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1019042 0.39116E-01     -380.0627883 0.49629E-02     -380.0677513   7.198   7.187   2.508  57.816
        Known (#6)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -380.0677513 0.49629E-02    -380.0627883 0.39116E-01    -380.1019042   7.198   7.187   2.508  57.816
   4     -380.1019042 0.81702E-02    -380.0937340  11.083        -391.1766914  24.118  23.693   2.542  57.050
   3     -391.1766914  5.1259        -386.0508087  2.6151        -388.6659386  10.039   9.083   8.096  17.909
   2     -388.6659386  2.0329        -386.6330395  3.8517        -390.4847275   6.906   6.726   5.146  28.177
   1     -390.4847275  5.5354        -384.9492931 0.55933E-01    -385.0052262  17.098  15.500   5.113  28.361

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

 Elapsed time=                                78.80
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             24206 time=          33.09 %= 42.0
 OPTIM> # of energy+gradient+Hessian calls=       318 time=           1.63 %=  2.1
