
 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)@comp30.ch.
                 Created on  5/28/12 at 10:30:21 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=    -379.9771294     RMS force=    0.9515581387E-06
 OPTIM> Final energy  =    -383.6175348     RMS force=    0.9718043069E-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      35.33320328    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     44223.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.33     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=    20
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    309 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    334 steps, energy/image=    -370.1293007     RMS=1.873988121     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   40.66     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0690 Dev= 3.65% S= 39.63 time= 6.36
 Following    2 images are candidates for TS:    5    9  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         61
 DNEB run yielded 2 true transition state(s) time=  10.04

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1016 steps. Energy=    -380.0725847       time=       2.28
 Minus side of path:                    1023 steps. Energy=    -383.5574802       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0725847 0.46861         -379.6039773  3.9535         -383.5574802  36.458  35.262   2.174  66.700
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    54   62 from     0.41196E-01 to     0.41217E-01 ref=     2.4353    
 checkperc> Increasing con cutoff atoms   105  108 from     0.25293E-01 to     0.25406E-01 ref=     2.0015    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     965 steps. Energy=    -382.5935568       time=       2.31
 Minus side of path:                     932 steps. Energy=    -382.1525243       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5935568 0.45078         -382.1427776 0.97467E-02     -382.1525243  11.137  11.020   2.376  61.038
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    75   76 from     0.71061E-02 to     0.74766E-02 ref=     1.5205    
 checkperc> Increasing con cutoff atoms    77   78 from     0.19067E-01 to     0.19153E-01 ref=     2.2474    
 checkperc> Increasing con cutoff atoms    75   76 from     0.74766E-02 to     0.77277E-02 ref=     1.5205    
 checkperc> Increasing con cutoff atoms    75   78 from     0.42237E-01 to     0.42771E-01 ref=     2.4372    
 checkperc> Increasing con cutoff atoms    75   79 from     0.77395E-01 to     0.79242E-01 ref=     2.5315    
 checkperc> Increasing con cutoff atoms    75   80 from     0.35113E-01 to     0.36092E-01 ref=     3.8147    
 checkperc> Increasing con cutoff atoms    77   78 from     0.19153E-01 to     0.20570E-01 ref=     2.2474    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4.3737    
 decide> The unconnected minima in the chain and their distances are:
     2        1.48     4     3        1.04     1 
 

 tryconnect> Interpolation for minima 2_F and 4_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=   145
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -379.6838393     RMS=.1955802224     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   2.449     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0262 Dev= 0.95% S= 1.48 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.46

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     892 steps. Energy=    -383.5574802       time=       2.04
 Minus side of path:                     875 steps. Energy=    -383.6175348       time=       1.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5574802 0.11483E-01     -383.5459977 0.71537E-01     -383.6175348   1.495   1.479   3.330  43.541
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=   145
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -376.1737258     RMS=.6593088237E-01 images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   1.777     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0376 Dev= 1.32% S= 1.04 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.44

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     949 steps. Energy=    -380.0725847       time=       2.60
 Minus side of path:                     944 steps. Energy=    -379.9771294       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0725847 0.11145         -379.9611372 0.15992E-01     -379.9771294   1.043   1.040  40.021   3.623
        Known (#3)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -379.9771294 0.15992E-01    -379.9611372 0.11145        -380.0725847   1.043   1.040  40.021   3.623
   1     -380.0725847 0.46861        -379.6039773  3.9535        -383.5574802  36.458  35.262   2.174  66.700
   3     -383.5574802 0.11483E-01    -383.5459977 0.71537E-01    -383.6175348   1.495   1.479   3.330  43.541

 Number of TS in the path       =      3
 Number of cycles               =      2

 Elapsed time=                                40.99
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             16823 time=          20.28 %= 49.5
 OPTIM> # of energy+gradient+Hessian calls=       121 time=           0.54 %=  1.3
