
 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 12:52: 4 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=    -392.1976999     RMS force=    0.8619930222E-06
 OPTIM> Final energy  =    -394.4130237     RMS force=    0.9481290240E-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=     4105.4    
 decide> The unconnected minima in the chain and their distances are:
     2       16.01     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 2.6935 Dev= 0.44% S= 21.40 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   6.41

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     858 steps. Energy=    -393.4575834       time=       2.39
 Minus side of path:                     892 steps. Energy=    -393.5530024       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4575834 0.70828E-03     -393.4568752 0.96127E-01     -393.5530024   1.382   1.381   2.091  69.343
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4303.7    
 decide> The unconnected minima in the chain and their distances are:
     2        4.29     4     3       16.17     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1115 Dev= 0.03% S= 4.33 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.53

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     971 steps. Energy=    -394.4130237       time=       2.87
 Minus side of path:                     923 steps. Energy=    -393.5530024       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4130237  1.0099         -393.4031315 0.14987         -393.5530024   4.675   4.287   5.223  27.763
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 3.8315 Dev= 17.17% S= 22.38 time= 0.79
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   7.38

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     910 steps. Energy=    -394.3423436       time=       2.46
 Minus side of path:                     935 steps. Energy=    -394.4130237       time=       2.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3423436 0.46911E-02     -394.3376525 0.75371E-01     -394.4130237   1.328   1.324   2.327  62.307
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3978.0    
 decide> The unconnected minima in the chain and their distances are:
     5       15.84     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 0.6772 Dev= 0.48% S= 21.37 time= 0.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   7.32

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     876 steps. Energy=    -392.0956502       time=       2.73
 Minus side of path:                     910 steps. Energy=    -392.1976999       time=       2.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.0956502 0.13473E-01     -392.0821772 0.11552         -392.1976999   1.018   1.015  39.392   3.681
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3971.8    
 decide> The unconnected minima in the chain and their distances are:
     5       15.84     6 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 6_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 1.2054 Dev= 0.50% S= 21.33 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.61

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     883 steps. Energy=    -394.5497349       time=       3.05
 Minus side of path:                     928 steps. Energy=    -394.6523294       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5497349 0.13243E-01     -394.5364916 0.11584         -394.6523294   1.017   1.014  39.326   3.687
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     3796.6    
 decide> The unconnected minima in the chain and their distances are:
     5       13.58     7     8       10.90     1 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 1.5115 Dev= 5.84% S= 19.37 time= 0.81
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   6.64
 isnewts> transition state is the same as number        5 energy=     -394.5364915540
 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:                     865 steps. Energy=    -394.5497349       time=       2.81
 Minus side of path:                     916 steps. Energy=    -394.6523294       time=       3.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5497349 0.13243E-01     -394.5364916 0.11584         -394.6523294   1.017   1.014  39.314   3.688
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2049 Dev= 0.17% S= 11.37 time= 0.44
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     951 steps. Energy=    -394.6523294       time=       2.42
 Minus side of path:                     928 steps. Energy=    -392.1976999       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6523294  3.3315         -391.3208421 0.87686         -392.1976999  12.054  10.902  19.150   7.572
        Known (#8)                                              Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2520.2    
 decide> The unconnected minima in the chain and their distances are:
     5       13.61     8 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 8_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 1.0343 Dev= 3.23% S= 19.27 time= 0.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   5.32
 isnewts> transition state is the same as number        5 energy=     -394.5364915537
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2617.8    
 decide> The unconnected minima in the chain and their distances are:
     2       13.78     7 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 7_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 1.8092 Dev= 1.66% S= 19.38 time= 0.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   6.68

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1027 steps. Energy=    -394.6523294       time=       2.83
 Minus side of path:                    1002 steps. Energy=    -394.4130237       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6523294  9.2070         -385.4453290  8.9677         -394.4130237  35.431  13.875   9.994  14.509
        Known (#8)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -392.1976999 0.87686        -391.3208421  3.3315        -394.6523294  12.054  10.902  19.150   7.572
   8     -394.6523294  9.2070        -385.4453290  8.9677        -394.4130237  35.431  13.875   9.994  14.509

 Number of TS in the path       =      2
 Number of cycles               =      7

 Elapsed time=                               104.54
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             28070 time=          38.28 %= 36.6
 OPTIM> # of energy+gradient+Hessian calls=       446 time=           2.25 %=  2.1
