
 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 13:12:10 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.3282199     RMS force=    0.9113233431E-06
 OPTIM> Final energy  =    -385.3812752     RMS force=    0.9782931898E-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=     93196.    
 decide> The unconnected minima in the chain and their distances are:
     2       45.34     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.1252 Dev= 2.67% S= 53.54 time= 7.37
 Following    1 images are candidates for TS:    7  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   8.13

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1028 steps. Energy=    -386.2227366       time=       3.34
 Minus side of path:                    1184 steps. Energy=    -385.3812752       time=       5.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2227366  5.1943         -381.0284168  4.3529         -385.3812752  41.872  40.574   1.999  72.554
        *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=     4120.9    
 decide> The unconnected minima in the chain and their distances are:
     3       16.03     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.1616 Dev= 0.29% S= 16.61 time= 0.69
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.63

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1502 steps. Energy=    -387.1746544       time=       8.79
 Minus side of path:                    1013 steps. Energy=    -386.2227366       time=       3.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  6.7566         -380.4180171  5.8047         -386.2227366  44.977  25.653   4.573  31.710
        *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      2 steps with      1 missing connections, weight=     8241.9    
 decide> The unconnected minima in the chain and their distances are:
     3       16.03     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 805 RMS= 0.0360 Dev= 4.97% S= 27.97 time= 22.10
 Following    3 images are candidates for TS:    2    9   18  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         41
 Converged to TS (number of iterations):         17
 DNEB run yielded 3 true transition state(s) time=  13.43

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1001 steps. Energy=    -383.3282199       time=       3.22
 Minus side of path:                    1028 steps. Energy=    -383.9584427       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.3282199 0.12796         -383.2002630 0.75818         -383.9584427   8.565   8.500   2.076  69.855
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1030 steps. Energy=    -384.3101967       time=       2.48
 Minus side of path:                    1016 steps. Energy=    -384.0989856       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3101967  4.8268         -379.4834245  4.6156         -384.0989856  27.049  15.397   2.538  57.135
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     991 steps. Energy=    -384.3101967       time=       2.47
 Minus side of path:                     987 steps. Energy=    -386.2227366       time=       3.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3101967 0.95086         -383.3593395  2.8634         -386.2227366   9.462   9.162   3.737  38.799
        Known (#6)                                              Known (#3)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     40.717    
 decide> The unconnected minima in the chain and their distances are:
     7        3.44     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 7_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0517 Dev= 0.05% S= 3.46 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.89

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     987 steps. Energy=    -384.0989856       time=       2.35
 Minus side of path:                     960 steps. Energy=    -383.9584427       time=       2.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856 0.19750         -383.9014855 0.56957E-01     -383.9584427   3.488   3.440  10.950  13.242
        Known (#7)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -383.3282199 0.12796        -383.2002630 0.75818        -383.9584427   8.565   8.500   2.076  69.855
   6     -383.9584427 0.56957E-01    -383.9014855 0.19750        -384.0989856   3.488   3.440  10.950  13.242
   4     -384.0989856  4.6156        -379.4834245  4.8268        -384.3101967  27.049  15.397   2.538  57.135
   5     -384.3101967 0.95086        -383.3593395  2.8634        -386.2227366   9.462   9.162   3.737  38.799
   1     -386.2227366  5.1943        -381.0284168  4.3529        -385.3812752  41.872  40.574   1.999  72.554

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                               103.05
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             44069 time=          50.53 %= 49.0
 OPTIM> # of energy+gradient+Hessian calls=       213 time=           1.01 %=  1.0
