
 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)@comp28.ch.
                 Created on  5/28/12 at 12:40:19 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=    -383.7841128     RMS force=    0.9398509944E-06
 OPTIM> Final energy  =    -380.7171662     RMS force=    0.9397297051E-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=     20195.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.23     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1808 Dev= 1.90% S= 32.75 time= 2.93
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.51

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1023 steps. Energy=    -380.9853352       time=       3.45
 Minus side of path:                    1012 steps. Energy=    -381.2610236       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9853352  2.1148         -378.8705102  2.3905         -381.2610236  22.439  18.762  15.856   9.145
        *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=     1809.4    
 decide> The unconnected minima in the chain and their distances are:
     2       11.92     4     3        4.84     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2205 Dev= 0.50% S= 12.57 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        155
 DNEB run yielded 1 true transition state(s) time=  13.41

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1068 steps. Energy=    -384.8130348       time=       3.92
 Minus side of path:                    1012 steps. Energy=    -383.7841128       time=       3.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8130348  1.5236         -383.2894568 0.49466         -383.7841128  44.545  40.566   2.174  66.702
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S 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= 0.2685 Dev= 0.31% S= 5.18 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.46

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     990 steps. Energy=    -383.7841128       time=       2.22
 Minus side of path:                     965 steps. Energy=    -380.9853352       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7841128  3.5603         -380.2238166 0.76152         -380.9853352   5.522   4.846  41.546   3.490
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3391.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.92     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0579 Dev= 7.18% S= 21.56 time= 22.51
 Following    2 images are candidates for TS:    6   14  
 Converged to TS (number of iterations):         56
 Converged to TS (number of iterations):         62
 DNEB run yielded 2 true transition state(s) time=  14.92
 isnewts> transition state is the same as number        3 energy=     -380.2238165873
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1071 steps. Energy=    -383.7841128       time=       4.45
 Minus side of path:                     991 steps. Energy=    -380.7171662       time=       3.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7841128  3.8783         -379.9058591 0.81131         -380.7171662  30.479  27.508  13.108  11.062
        Known (#1)                                              Known (#2)

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     944 steps. Energy=    -380.9853352       time=       3.09
 Minus side of path:                     997 steps. Energy=    -383.7841128       time=       3.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9853352 0.76152         -380.2238166  3.5603         -383.7841128   5.528   4.853  41.071   3.530
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -383.7841128  3.8783        -379.9058591 0.81131        -380.7171662  30.479  27.508  13.108  11.062

 Number of TS in the path       =      1
 Number of cycles               =      3

 Elapsed time=                                95.96
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             36957 time=          43.32 %= 45.1
 OPTIM> # of energy+gradient+Hessian calls=       335 time=           1.54 %=  1.6
