
 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)@comp35.ch.
                 Created on  5/28/12 at 10:29:47 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=    -398.1927016     RMS force=    0.8486334885E-06
 OPTIM> Final energy  =    -399.2373900     RMS force=    0.9631529387E-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      43.77249097    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     4479.0    
 decide> The unconnected minima in the chain and their distances are:
     2       16.44     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=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     80 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    105 steps, energy/image=    -321.9631083     RMS=13.45276474     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   27.79     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 280 RMS= 0.0618 Dev= 1.00% S= 21.04 time= 3.34
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   6.53

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     923 steps. Energy=    -396.7319119       time=       3.38
 Minus side of path:                     936 steps. Energy=    -399.2373900       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7319119 0.49103         -396.2408831  2.9965         -399.2373900  15.675  12.327   3.444  42.096
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    13   26 from     0.22207E-01 to     0.24689E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms    27   30 from     0.38622E-01 to     0.44121E-01 ref=     2.4439    
 checkperc> Increasing con cutoff atoms    28   29 from     0.13593E-01 to     0.14539E-01 ref=     2.0966    
 checkperc> Increasing con cutoff atoms    29   30 from     0.72295E-02 to     0.76711E-02 ref=     1.5467    
 checkperc> Increasing con cutoff atoms   109  118 from     0.52595E-01 to     0.54220E-01 ref=     3.8494    
 checkperc> Increasing con cutoff atoms   111  113 from     0.24108E-01 to     0.25144E-01 ref=     2.4207    
 checkperc> Increasing con cutoff atoms   116  130 from     0.99179E-01 to     0.99415E-01 ref=     2.5363    
 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=     4478.5    
 decide> The unconnected minima in the chain and their distances are:
     3       16.47     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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     64 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     89 steps, energy/image=    -388.9256146     RMS=.7566370588     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   18.71     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 175 RMS= 0.1310 Dev= 0.68% S= 16.92 time= 1.30
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.15

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     930 steps. Energy=    -396.7319119       time=       3.20
 Minus side of path:                     936 steps. Energy=    -397.7050685       time=       3.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7319119 0.18843         -396.5434769  1.1616         -397.7050685  15.585  15.097   5.602  25.884
        Known (#3)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    29   30 from     0.76711E-02 to     0.89595E-02 ref=     1.5467    
 checkperc> Increasing con cutoff atoms    29   33 from     0.24294E-01 to     0.28141E-01 ref=     2.5627    
 checkperc> Increasing con cutoff atoms   109  115 from     0.39032E-01 to     0.41646E-01 ref=     2.3999    
 checkperc> Increasing con cutoff atoms   116  130 from     0.99415E-01 to     0.10826     ref=     2.5363    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     204.31    
 decide> The unconnected minima in the chain and their distances are:
     4        5.88     1 
 

 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=   140
 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=    -393.7749828     RMS=.1865841100     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   7.783     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.1283 Dev= 0.34% S= 5.90 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     827 steps. Energy=    -397.7050685       time=       2.07
 Minus side of path:                     942 steps. Energy=    -398.1927016       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.7050685 0.13339E-04     -397.7050552 0.48765         -398.1927016   5.937   5.884   3.294  44.019
        Known (#4)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -398.1927016 0.48765        -397.7050552 0.13339E-04    -397.7050685   5.937   5.884   3.294  44.019
   2     -397.7050685  1.1616        -396.5434769 0.18843        -396.7319119  15.585  15.097   5.602  25.884
   1     -396.7319119 0.49103        -396.2408831  2.9965        -399.2373900  15.675  12.327   3.444  42.096

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

 Elapsed time=                                38.15
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             11696 time=          16.84 %= 44.1
 OPTIM> # of energy+gradient+Hessian calls=       124 time=           0.62 %=  1.6
