
 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)@comp33.ch.
                 Created on  5/28/12 at 13:12:42 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=    -389.8328792     RMS force=    0.9213414051E-06
 OPTIM> Final energy  =    -394.4192763     RMS force=    0.8976902090E-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=     20427.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.34     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.3914 Dev= 1.66% S= 29.33 time= 3.35
 Following    2 images are candidates for TS:    4    6  
 Converged to TS (number of iterations):         59
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=  11.07

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     926 steps. Energy=    -392.8445366       time=       3.46
 Minus side of path:                     961 steps. Energy=    -389.8260034       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8445366  3.6822         -389.1622948 0.66371         -389.8260034  28.013  26.212   2.598  55.809
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     887 steps. Energy=    -398.5496307       time=       2.56
 Minus side of path:                     878 steps. Energy=    -394.4192763       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.5496307  4.7772         -393.7724351 0.64684         -394.4192763   7.229   6.148   8.734  16.601
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     287.21    
 decide> The unconnected minima in the chain and their distances are:
     5        6.59     3     4        1.09     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3229 Dev= 0.79% S= 7.00 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.49

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     868 steps. Energy=    -392.8445366       time=       2.85
 Minus side of path:                     872 steps. Energy=    -392.8644444       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8445366 0.18206E-01     -392.8263302 0.38114E-01     -392.8644444   3.087   2.894  28.762   5.041
        Known (#3)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0061 Dev= 0.03% S= 1.09 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     904 steps. Energy=    -389.8260034       time=       2.39
 Minus side of path:                     921 steps. Energy=    -389.8328792       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.8260034 0.61890E-02     -389.8198144 0.13065E-01     -389.8328792   1.090   1.090   2.785  52.073
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     398.77    
 decide> The unconnected minima in the chain and their distances are:
     5        7.36     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.1512 Dev= 0.51% S= 7.93 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     810 steps. Energy=    -392.8681296       time=       2.31
 Minus side of path:                     804 steps. Energy=    -392.8644444       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8681296 0.13432E-01     -392.8546981 0.97463E-02     -392.8644444   2.690   2.647  38.891   3.728
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     267.74    
 decide> The unconnected minima in the chain and their distances are:
     5        6.45     7 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.2389 Dev= 0.41% S= 6.90 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.66
 isnewts> transition state is the same as number        5 energy=     -392.8546980999
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     803 steps. Energy=    -392.8681296       time=       2.34
 Minus side of path:                     803 steps. Energy=    -392.8644444       time=       1.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8681296 0.13432E-01     -392.8546981 0.97463E-02     -392.8644444   2.690   2.647  38.903   3.727
        Known (#7)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     429.47    
 decide> The unconnected minima in the chain and their distances are:
     2        7.54     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1189 Dev= 0.11% S= 7.62 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.63

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     931 steps. Energy=    -394.4192763       time=       2.28
 Minus side of path:                     913 steps. Energy=    -392.8681296       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4192763  3.5335         -390.8857681  1.9824         -392.8681296   8.031   7.547  21.269   6.817
        Known (#2)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -389.8328792 0.13065E-01    -389.8198144 0.61890E-02    -389.8260034   1.090   1.090   2.785  52.073
   1     -389.8260034 0.66371        -389.1622948  3.6822        -392.8445366  28.013  26.212   2.598  55.809
   3     -392.8445366 0.18206E-01    -392.8263302 0.38114E-01    -392.8644444   3.087   2.894  28.762   5.041
   5     -392.8644444 0.97463E-02    -392.8546981 0.13432E-01    -392.8681296   2.690   2.647  38.891   3.728
   7     -392.8681296  1.9824        -390.8857681  3.5335        -394.4192763   8.031   7.547  21.269   6.817

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

 Elapsed time=                                73.66
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21674 time=          31.58 %= 42.9
 OPTIM> # of energy+gradient+Hessian calls=       261 time=           1.37 %=  1.9
