
 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)@comp35.ch.
                 Created on  5/28/12 at 13: 8:34 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -376.2671042     RMS force=    0.8865544979E-06
 OPTIM> Final energy  =    -380.2167143     RMS force=    0.8536262175E-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=     37053.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.34     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0811 Dev= 2.57% S= 36.67 time= 4.21
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):        186
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=  27.14

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1015 steps. Energy=    -376.7437409       time=       3.02
 Minus side of path:                    1193 steps. Energy=    -376.2671042       time=       3.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.7437409  1.8116         -374.9321329  1.3350         -376.2671042  32.451  30.818   2.086  69.525
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     986 steps. Energy=    -380.2167143       time=       2.63
 Minus side of path:                    1179 steps. Energy=    -379.8505499       time=       4.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2167143  1.8176         -378.3991084  1.4514         -379.8505499  31.813  30.269   2.072  69.992
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     733.34    
 decide> The unconnected minima in the chain and their distances are:
     2        9.02     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5100 Dev= 0.24% S= 9.33 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.81

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     955 steps. Energy=    -376.1432362       time=       3.53
 Minus side of path:                    1014 steps. Energy=    -376.7437409       time=       3.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.1432362  1.4841         -374.6590986  2.0846         -376.7437409   7.868   6.321  12.859  11.276
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 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=     51.573    
 decide> The unconnected minima in the chain and their distances are:
     2        3.72     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1393 Dev= 0.07% S= 3.96 time= 0.25
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   4.66

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     962 steps. Energy=    -377.6974406       time=       2.43
 Minus side of path:                     943 steps. Energy=    -380.2553741       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.6974406 0.36404         -377.3334015  2.9220         -380.2553741   3.739   2.856  23.455   6.182
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     22.312    
 decide> The unconnected minima in the chain and their distances are:
     2        1.31     7     6        2.72     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0192 Dev= 0.11% S= 1.31 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.70

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     939 steps. Energy=    -380.2167143       time=       2.95
 Minus side of path:                     948 steps. Energy=    -380.2553741       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2167143 0.31773E-01     -380.1849415 0.70433E-01     -380.2553741   1.313   1.307  24.431   5.935
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1514 Dev= 0.43% S= 2.79 time= 0.23
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.84

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     969 steps. Energy=    -377.6974406       time=       3.01
 Minus side of path:                     939 steps. Energy=    -376.2376627       time=       3.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.6974406  1.4895         -376.2079712 0.29691E-01     -376.2376627   2.697   2.658  26.251   5.524
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=    0.99885    
 decide> The unconnected minima in the chain and their distances are:
     8        1.00     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0199 Dev= 0.23% S= 1.01 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     952 steps. Energy=    -376.2376627       time=       2.91
 Minus side of path:                     937 steps. Energy=    -376.1432362       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.2376627 0.10469         -376.1329736 0.10263E-01     -376.1432362   1.003   1.000  15.301   9.476
        Known (#8)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -376.2671042  1.3350        -374.9321329  1.8116        -376.7437409  32.451  30.818   2.086  69.525
   3     -376.7437409  2.0846        -374.6590986  1.4841        -376.1432362   7.868   6.321  12.859  11.276
   7     -376.1432362 0.10263E-01    -376.1329736 0.10469        -376.2376627   1.003   1.000  15.301   9.476
   6     -376.2376627 0.29691E-01    -376.2079712  1.4895        -377.6974406   2.697   2.658  26.251   5.524
   4     -377.6974406 0.36404        -377.3334015  2.9220        -380.2553741   3.739   2.856  23.455   6.182
   5     -380.2553741 0.70433E-01    -380.1849415 0.31773E-01    -380.2167143   1.313   1.307  24.431   5.935

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                                96.87
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26106 time=          31.19 %= 32.2
 OPTIM> # of energy+gradient+Hessian calls=       301 time=           1.46 %=  1.5
