
 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)@comp23.ch.
                 Created on  5/28/12 at 13:11:36 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -393.3564342     RMS force=    0.9803809862E-06
 OPTIM> Final energy  =    -395.0101498     RMS force=    0.9098875046E-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=     790.11    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4318 Dev= 0.29% S= 9.39 time= 0.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.54

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     861 steps. Energy=    -393.3564342       time=       2.03
 Minus side of path:                    1103 steps. Energy=    -396.5791634       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3564342 0.21102         -393.1454182  3.4337         -396.5791634  20.925  20.237   3.851  37.655
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1580.2    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 2_F using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2575150228    
 Double-ended search iterations= 735 RMS= 0.0115 Dev= 6.99% S= 14.77 time= 22.89
 Following    2 images are candidates for TS:    3   20  
 Converged to TS (number of iterations):         13
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   6.39
 isnewts> transition state is the same as number        1 energy=     -393.1454181851
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     851 steps. Energy=    -393.3564342       time=       2.62
 Minus side of path:                    1094 steps. Energy=    -396.5791634       time=       4.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3564342 0.21102         -393.1454182  3.4337         -396.5791634  20.924  20.236   3.856  37.601
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     896 steps. Energy=    -395.0101498       time=       2.92
 Minus side of path:                     864 steps. Energy=    -395.3584522       time=       2.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0101498 0.17815         -394.8320003 0.52645         -395.3584522   3.801   3.460   2.712  53.464
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     441.84    
 decide> The unconnected minima in the chain and their distances are:
     4        7.62     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2997 Dev= 0.13% S= 7.75 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.45
 isnewts> transition state is the same as number        1 energy=     -393.1454181852
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     883.67    
 decide> The unconnected minima in the chain and their distances are:
     4        7.62     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 4_F using 17 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 595 RMS= 0.0249 Dev= 3.10% S= 9.42 time= 15.00
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.64
 isnewts> transition state is the same as number        1 energy=     -393.1454181852
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1325.5    
 decide> The unconnected minima in the chain and their distances are:
     4        7.62     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 805 RMS= 0.0286 Dev= 5.62% S= 11.10 time= 27.74
 Following    2 images are candidates for TS:    3   19  
 Converged to TS (number of iterations):         13
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   6.36
 isnewts> transition state is the same as number        1 energy=     -393.1454181851
 tryconnect> Will not repeat search for TS      1 same as TS      1

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1020 steps. Energy=    -396.5791634       time=       4.15
 Minus side of path:                     809 steps. Energy=    -395.3584522       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.5791634  1.2406         -395.3385587 0.19893E-01     -395.3584522  19.355  19.023   3.563  40.694
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -393.3564342 0.21102        -393.1454182  3.4337        -396.5791634  20.925  20.237   3.851  37.655
   4     -396.5791634  1.2406        -395.3385587 0.19893E-01    -395.3584522  19.355  19.023   3.563  40.694
   3     -395.3584522 0.52645        -394.8320003 0.17815        -395.0101498   3.801   3.460   2.712  53.464

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               114.57
 OPTIM> # of energy calls=                        130 time=           0.18 %=  0.2
 OPTIM> # of energy+gradient calls=             57719 time=          82.33 %= 71.9
 OPTIM> # of energy+gradient+Hessian calls=       125 time=           0.65 %=  0.6
