
 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 10:31:57 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=    -392.6369392     RMS force=    0.9549745018E-06
 OPTIM> Final energy  =    -391.7065242     RMS force=    0.9877291348E-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      57.06092791    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     4257.7    
 decide> The unconnected minima in the chain and their distances are:
     2       16.15     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=    75
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=     3071.963856     RMS=19.91184458     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   25.60     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 245 RMS= 0.5726 Dev= 2.03% S= 23.27 time= 2.51
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.08

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     912 steps. Energy=    -391.9882572       time=       2.23
 Minus side of path:                     910 steps. Energy=    -391.7065242       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9882572 0.48906         -391.4992007 0.20732         -391.7065242   4.081   3.251  12.201  11.884
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3847.3    
 decide> The unconnected minima in the chain and their distances are:
     3       15.61     1 
 

 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=    79
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    123 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    148 steps, energy/image=    -369.9754015     RMS=1.775311492     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   21.22     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 210 RMS= 0.2084 Dev= 0.92% S= 21.75 time= 1.79
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   5.51
 isnewts> transition state is the same as number        1 energy=     -391.4992006717
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     939 steps. Energy=    -391.9882572       time=       2.29
 Minus side of path:                     919 steps. Energy=    -391.7065242       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9882572 0.48906         -391.4992007 0.20732         -391.7065242   4.081   3.251  12.197  11.888
        Known (#3)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     7694.5    
 decide> The unconnected minima in the chain and their distances are:
     3       15.61     1 
 

 tryconnect> Interpolation for minima 1_S and 3_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    79
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     70 fraction=    0.990000 images=    15 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     95 steps, energy/image=     55.11520342     RMS=2.996891641     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   29.71     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 805 RMS= 0.0886 Dev= 5.02% S= 30.72 time= 26.11
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.05

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     964 steps. Energy=    -392.4143163       time=       2.38
 Minus side of path:                    1052 steps. Energy=    -392.6369392       time=       2.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4143163  3.8528         -388.5615237  4.0754         -392.6369392  30.881  24.441   2.465  58.834
        *NEW* (Placed in 4)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    14   22 from     0.31014E-01 to     0.32012E-01 ref=     4.9065    
 checkperc> Increasing con cutoff atoms    15   17 from     0.41078E-02 to     0.42953E-02 ref=     2.1268    
 checkperc> Increasing con cutoff atoms    15   22 from     0.13294E-01 to     0.13536E-01 ref=     3.4463    
 checkperc> Increasing con cutoff atoms    15   24 from     0.19081E-01 to     0.19088E-01 ref=     4.0220    
 checkperc> Increasing con cutoff atoms    17   23 from     0.42505E-02 to     0.44869E-02 ref=     2.7037    
 checkperc> Increasing con cutoff atoms    89   91 from     0.66421E-02 to     0.68058E-02 ref=     1.3375    
 checkperc> Increasing con cutoff atoms    96   98 from     0.17795E-02 to     0.20831E-02 ref=     1.3736    
 checkperc> Increasing con cutoff atoms   105  107 from     0.65849E-02 to     0.70556E-02 ref=     1.3318    
 checkperc> Increasing con cutoff atoms   105  108 from     0.21373E-01 to     0.21871E-01 ref=     2.0042    
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1799.6    
 decide> The unconnected minima in the chain and their distances are:
     2       12.15     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S 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=    99
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     49 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     74 steps, energy/image=    -354.9014691     RMS=13.83400181     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   17.68     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 0.0425 Dev= 0.49% S= 12.21 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.86

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     910 steps. Energy=    -391.7065242       time=       2.28
 Minus side of path:                     917 steps. Energy=    -392.4143163       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7065242 0.24756         -391.4589636 0.95535         -392.4143163  12.673  12.151   2.400  60.413
        Known (#2)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -392.6369392  4.0754        -388.5615237  3.8528        -392.4143163  30.881  24.441   2.465  58.834
   4     -392.4143163 0.95535        -391.4589636 0.24756        -391.7065242  12.673  12.151   2.400  60.413

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

 Elapsed time=                                74.81
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             34384 time=          46.45 %= 62.1
 OPTIM> # of energy+gradient+Hessian calls=       224 time=           1.11 %=  1.5
