
 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)@comp34.ch.
                 Created on  5/28/12 at 13: 1:32 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=    -391.4617264     RMS force=    0.9202775967E-06
 OPTIM> Final energy  =    -391.2684032     RMS force=    0.9870640645E-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=     27228.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.08     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 315 RMS= 0.1413 Dev= 0.88% S= 35.22 time= 4.47
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.45
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     54456.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.08     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 805 RMS= 0.0673 Dev= 6.82% S= 43.04 time= 28.00
 Following    3 images are candidates for TS:    4    8   13  
 Converged to TS (number of iterations):         46
 Converged to TS (number of iterations):         57
 Converged to TS (number of iterations):         71
 DNEB run yielded 3 true transition state(s) time=  17.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     886 steps. Energy=    -391.4617264       time=       2.44
 Minus side of path:                     930 steps. Energy=    -393.6609809       time=       2.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4617264 0.20702         -391.2547094  2.4063         -393.6609809  12.145  11.189   4.884  29.687
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     916 steps. Energy=    -391.2244416       time=       2.79
 Minus side of path:                     868 steps. Energy=    -391.1689352       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2244416 0.12374         -391.1007010 0.68234E-01     -391.1689352   7.511   7.098   2.463  58.875
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1249 steps. Energy=    -391.2684032       time=       6.81
 Minus side of path:                     910 steps. Energy=    -391.4356342       time=       3.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2684032  1.4104         -389.8580234  1.5776         -391.4356342  30.118  26.863   2.350  61.696
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1172.0    
 decide> The unconnected minima in the chain and their distances are:
     6       10.06     4     5        5.37     3 
 

 tryconnect> 105-iteration DNEB run for minima 4_U and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1009 Dev= 0.61% S= 10.18 time= 0.52
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   5.75

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     862 steps. Energy=    -391.4356342       time=       3.60
 Minus side of path:                     877 steps. Energy=    -392.0698724       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342 0.69070         -390.7449373  1.3249         -392.0698724   3.649   3.439  16.448   8.816
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3205 Dev= 0.87% S= 5.45 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     903 steps. Energy=    -391.1689352       time=       3.18
 Minus side of path:                     913 steps. Energy=    -393.6609809       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1689352 0.64227         -390.5266678  3.1343         -393.6609809   5.856   5.369   7.343  19.745
        Known (#5)                                              Known (#3)
 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      6 steps with      1 missing connections, weight=     775.42    
 decide> The unconnected minima in the chain and their distances are:
     7        9.19     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0311 Dev= 0.34% S= 9.20 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.10

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     923 steps. Energy=    -391.2244416       time=       2.34
 Minus side of path:                     878 steps. Energy=    -392.0698724       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2244416 0.11860         -391.1058370 0.96404         -392.0698724   9.552   9.188   2.406  60.271
        Known (#4)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -391.4617264 0.20702        -391.2547094  2.4063        -393.6609809  12.145  11.189   4.884  29.687
   5     -393.6609809  3.1343        -390.5266678 0.64227        -391.1689352   5.856   5.369   7.343  19.745
   2     -391.1689352 0.68234E-01    -391.1007010 0.12374        -391.2244416   7.511   7.098   2.463  58.875
   6     -391.2244416 0.11860        -391.1058370 0.96404        -392.0698724   9.552   9.188   2.406  60.271
   4     -392.0698724  1.3249        -390.7449373 0.69070        -391.4356342   3.649   3.439  16.448   8.816
   3     -391.4356342  1.5776        -389.8580234  1.4104        -391.2684032  30.118  26.863   2.350  61.696

 Number of TS in the path       =      6
 Number of cycles               =      4

 Elapsed time=                               125.86
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             40226 time=          59.48 %= 47.3
 OPTIM> # of energy+gradient+Hessian calls=       505 time=           2.80 %=  2.2
