
 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)@comp29.ch.
                 Created on  5/28/12 at 12:36:25 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -393.7903615     RMS force=    0.8939806970E-06
 OPTIM> Final energy  =    -388.1436370     RMS force=    0.9895757446E-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=     11972.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.88     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1732 Dev= 0.25% S= 25.36 time= 1.79
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.05

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1051 steps. Energy=    -390.9334808       time=       4.09
 Minus side of path:                    1053 steps. Energy=    -388.1436370       time=       3.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9334808  5.4814         -385.4521111  2.6915         -388.1436370  25.377  23.321   5.053  28.697
        *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=     711.12    
 decide> The unconnected minima in the chain and their distances are:
     3        8.93     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1617 Dev= 0.08% S= 9.09 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   4.94

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     914 steps. Energy=    -390.9334808       time=       3.57
 Minus side of path:                    1472 steps. Energy=    -398.3674514       time=       5.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9334808 0.38173         -390.5517528  7.8157         -398.3674514  24.850  23.443   2.198  65.982
        Known (#3)                                              *NEW* (Placed in 4)
 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=     1422.2    
 decide> The unconnected minima in the chain and their distances are:
     3        8.93     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 3_F using 20 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 700 RMS= 0.0499 Dev= 6.00% S= 11.93 time= 19.88
 Following    1 images are candidates for TS:   19  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.58
 isnewts> transition state is the same as number        2 energy=     -390.5517527757
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1477 steps. Energy=    -398.3674514       time=       7.22
 Minus side of path:                     933 steps. Energy=    -390.9334808       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.3674514  7.8157         -390.5517528 0.38173         -390.9334808  24.850  23.442   2.198  65.958
        Known (#4)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2133.4    
 decide> The unconnected minima in the chain and their distances are:
     3        8.93     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0293 Dev= 5.06% S= 13.50 time= 26.41
 Following    1 images are candidates for TS:   21  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.63
 isnewts> transition state is the same as number        2 energy=     -390.5517527756
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     20642.    
 decide> The unconnected minima in the chain and their distances are:
     4       27.43     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1168 Dev= 2.16% S= 30.49 time= 3.21
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   8.32

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     965 steps. Energy=    -393.7136465       time=       3.36
 Minus side of path:                    1333 steps. Energy=    -399.2994549       time=       5.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7136465 0.60658         -393.1070615  6.1924         -399.2994549  32.053  24.068   2.082  69.657
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     339.09    
 decide> The unconnected minima in the chain and their distances are:
     4        5.34     6     5        5.71     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0924 Dev= 0.01% S= 5.44 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.80

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     833 steps. Energy=    -398.3674514       time=       2.51
 Minus side of path:                     842 steps. Energy=    -399.2994549       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.3674514 0.69472         -397.6727308  1.6267         -399.2994549   5.567   5.345  20.015   7.245
        Known (#4)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0381 Dev= 0.00% S= 5.72 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.55

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     855 steps. Energy=    -393.7136465       time=       3.24
 Minus side of path:                     887 steps. Energy=    -393.7903615       time=       2.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7136465 0.97259E-02     -393.7039205 0.86441E-01     -393.7903615   5.940   5.713   2.395  60.531
        Known (#5)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -393.7903615 0.86441E-01    -393.7039205 0.97259E-02    -393.7136465   5.940   5.713   2.395  60.531
   4     -393.7136465 0.60658        -393.1070615  6.1924        -399.2994549  32.053  24.068   2.082  69.657
   5     -399.2994549  1.6267        -397.6727308 0.69472        -398.3674514   5.567   5.345  20.015   7.245
   2     -398.3674514  7.8157        -390.5517528 0.38173        -390.9334808  24.850  23.443   2.198  65.982
   1     -390.9334808  5.4814        -385.4521111  2.6915        -388.1436370  25.377  23.321   5.053  28.697

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

 Elapsed time=                               132.79
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             55704 time=          76.86 %= 57.9
 OPTIM> # of energy+gradient+Hessian calls=       201 time=           1.04 %=  0.8
