
 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)@comp21.ch.
                 Created on  5/28/12 at 13:10:49 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 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)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0940 Dev= 1.12% S= 28.91 time= 3.39
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   8.55

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     910 steps. Energy=    -389.8260034       time=       2.25
 Minus side of path:                     919 steps. Energy=    -389.8328792       time=       2.30

         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  52.072
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     19845.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.07     3 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0810 Dev= 1.67% S= 29.01 time= 3.31
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         64
 DNEB run yielded 2 true transition state(s) time=  10.18

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     882 steps. Energy=    -398.5496307       time=       2.88
 Minus side of path:                     900 steps. Energy=    -394.4192763       time=       2.95

         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   8.729  16.611
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     921 steps. Energy=    -392.8445366       time=       3.07
 Minus side of path:                     945 steps. Energy=    -389.8260034       time=       3.11

         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  55.802
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     285.92    
 decide> The unconnected minima in the chain and their distances are:
     4        6.59     5 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3691 Dev= 0.19% S= 7.02 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        140
 DNEB run yielded 1 true transition state(s) time=  12.95

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     828 steps. Energy=    -390.9819266       time=       2.49
 Minus side of path:                     973 steps. Energy=    -394.1772191       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9819266 0.34693E-01     -390.9472337  3.2300         -394.1772191  16.521  15.888   4.277  33.905
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     471.01    
 decide> The unconnected minima in the chain and their distances are:
     2        7.78     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1227 Dev= 0.20% S= 7.86 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.87

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     923 steps. Energy=    -394.4192763       time=       3.68
 Minus side of path:                     916 steps. Energy=    -392.8681296       time=       3.91

         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  21.270   6.817
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1.0816    
 decide> The unconnected minima in the chain and their distances are:
     8        1.03     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.0056 Dev= 0.02% S= 1.03 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.50

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     853 steps. Energy=    -392.8681296       time=       2.28
 Minus side of path:                     733 steps. Energy=    -392.8445366       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8681296 0.24517E-01     -392.8436128 0.92387E-03     -392.8445366   1.029   1.026   3.274  44.283
        Known (#8)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.8328792 0.13065E-01    -389.8198144 0.61890E-02    -389.8260034   1.090   1.090   2.785  52.072
   3     -389.8260034 0.66371        -389.1622948  3.6822        -392.8445366  28.013  26.212   2.598  55.802
   6     -392.8445366 0.92387E-03    -392.8436128 0.24517E-01    -392.8681296   1.029   1.026   3.274  44.283
   5     -392.8681296  1.9824        -390.8857681  3.5335        -394.4192763   8.031   7.547  21.270   6.817

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

 Elapsed time=                                80.66
 OPTIM> # of energy calls=                         44 time=           0.06 %=  0.1
 OPTIM> # of energy+gradient calls=             21400 time=          31.08 %= 38.5
 OPTIM> # of energy+gradient+Hessian calls=       360 time=           2.02 %=  2.5
