
 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> Constraint potential parameters read from file congeom.dat
 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 10:31: 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -384.8119039     RMS force=    0.9802004810E-06
 OPTIM> Final energy  =    -384.6621550     RMS force=    0.9449818968E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      35.31331073    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     43565.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.15     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    30
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    142 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    167 steps, energy/image=    -375.1759879     RMS=1.554195402     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   39.90     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0551 Dev= 3.41% S= 40.74 time= 5.74
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         63
 DNEB run yielded 2 true transition state(s) time=  12.13

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     958 steps. Energy=    -385.9653714       time=       3.20
 Minus side of path:                    1148 steps. Energy=    -385.3728640       time=       4.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9653714  2.7211         -383.2443107  2.1286         -385.3728640  23.165  12.037   3.185  45.523
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    90   93 from     0.76096E-01 to     0.81182E-01 ref=     2.8077    
 checkperc> Increasing con cutoff atoms   132  133 from     0.35731E-02 to     0.35811E-02 ref=    0.98074    
 checkperc> Increasing con cutoff atoms    61   64 from     0.54822E-01 to     0.56830E-01 ref=     2.8053    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1026 steps. Energy=    -385.9653714       time=       3.58
 Minus side of path:                     948 steps. Energy=    -385.6241796       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9653714  1.8534         -384.1119856  1.5122         -385.6241796  19.937  18.434   2.735  53.025
        Known (#3)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    95   98 from     0.15770E-01 to     0.15902E-01 ref=     2.5188    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     9921.7    
 decide> The unconnected minima in the chain and their distances are:
     2       20.66     5     4       10.25     1 
 

 tryconnect> Interpolation for minima 2_F and 5_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    63
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     83 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    108 steps, energy/image=    -336.4783928     RMS=10.18073774     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   28.19     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 280 RMS= 0.1544 Dev= 0.63% S= 21.13 time= 3.01
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.09

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1146 steps. Energy=    -385.6241796       time=       4.40
 Minus side of path:                     971 steps. Energy=    -384.6621550       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.6241796  1.0440         -384.5802145 0.81941E-01     -384.6621550  22.642  20.669   3.018  48.044
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   108
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -375.1241730     RMS=2.279045733     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   17.63     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 0.0793 Dev= 1.07% S= 10.27 time= 1.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.31

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     951 steps. Energy=    -384.8119039       time=       3.36
 Minus side of path:                     933 steps. Energy=    -385.3728640       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8119039 0.59681E-01     -384.7522224 0.62064         -385.3728640  10.505  10.248   2.215  65.449
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -384.8119039 0.59681E-01    -384.7522224 0.62064        -385.3728640  10.505  10.248   2.215  65.449
   1     -385.3728640  2.1286        -383.2443107  2.7211        -385.9653714  23.165  12.037   3.185  45.523
   2     -385.9653714  1.8534        -384.1119856  1.5122        -385.6241796  19.937  18.434   2.735  53.025
   3     -385.6241796  1.0440        -384.5802145 0.81941E-01    -384.6621550  22.642  20.669   3.018  48.044

 Number of TS in the path       =      4
 Number of cycles               =      2

 Elapsed time=                                59.22
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             19709 time=          25.77 %= 43.5
 OPTIM> # of energy+gradient+Hessian calls=       144 time=           0.62 %=  1.1
