
 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: 9:20 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=    -383.9810874     RMS force=    0.9967696212E-06
 OPTIM> Final energy  =    -385.8649070     RMS force=    0.9817715371E-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=     41141.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.52     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= 0.0744 Dev= 2.91% S= 37.16 time= 4.34
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):         93
 Converged to TS (number of iterations):         82
 DNEB run yielded 2 true transition state(s) time=  14.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     975 steps. Energy=    -382.8545546       time=       2.42
 Minus side of path:                    1033 steps. Energy=    -385.8649070       time=       3.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.8545546 0.83671         -382.0178447  3.8471         -385.8649070  28.136  26.332   1.598  90.729
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     945 steps. Energy=    -385.8649070       time=       3.25
 Minus side of path:                    1047 steps. Energy=    -384.0550271       time=       2.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8649070  1.9858         -383.8790580 0.17597         -384.0550271  21.208  18.166   2.261  64.119
        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=     8575.4    
 decide> The unconnected minima in the chain and their distances are:
     4       20.47     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 3.8092 Dev= 0.15% S= 21.01 time= 1.57
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1062 steps. Energy=    -384.2152072       time=       2.60
 Minus side of path:                     999 steps. Energy=    -384.6463498       time=       3.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2152072  1.7528         -382.4624260  2.1839         -384.6463498  26.049  19.659   2.089  69.414
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     8056.6    
 decide> The unconnected minima in the chain and their distances are:
     4       19.92     6     5        5.29     1 
 

 tryconnect> 175-iteration DNEB run for minima 4_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0374 Dev= 0.03% S= 20.02 time= 1.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.30

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1026 steps. Energy=    -384.6463498       time=       2.50
 Minus side of path:                     926 steps. Energy=    -384.0549925       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6463498 0.68276         -383.9635886 0.91404E-01     -384.0549925  20.094  19.543   2.109  68.760
        Known (#6)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0383 Dev= 0.03% S= 5.31 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.12

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     980 steps. Energy=    -384.2152072       time=       2.51
 Minus side of path:                     991 steps. Energy=    -383.9810874       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2152072 0.74937         -383.4658404 0.51525         -383.9810874   5.514   5.293   6.032  24.039
        Known (#5)                                              Known (#1)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=    0.34875    
 decide> The unconnected minima in the chain and their distances are:
     4        0.70     7 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0050 Dev= 0.01% S= 0.70 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.67

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     934 steps. Energy=    -384.0549925       time=       2.18
 Minus side of path:                     904 steps. Energy=    -384.0550271       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0549925 0.31426E-02     -384.0518500 0.31771E-02     -384.0550271   0.706   0.704   3.182  45.565
        Known (#7)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -383.9810874 0.51525        -383.4658404 0.74937        -384.2152072   5.514   5.293   6.032  24.039
   3     -384.2152072  1.7528        -382.4624260  2.1839        -384.6463498  26.049  19.659   2.089  69.414
   4     -384.6463498 0.68276        -383.9635886 0.91404E-01    -384.0549925  20.094  19.543   2.109  68.760
   6     -384.0549925 0.31426E-02    -384.0518500 0.31771E-02    -384.0550271   0.706   0.704   3.182  45.565
   2     -384.0550271 0.17597        -383.8790580  1.9858        -385.8649070  21.208  18.166   2.261  64.119

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

 Elapsed time=                                68.70
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23506 time=          28.21 %= 41.1
 OPTIM> # of energy+gradient+Hessian calls=       266 time=           1.20 %=  1.7
