
 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     79
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     8
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)@comp33.ch.
                 Created on  5/28/12 at 12: 4: 6 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 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>  237 Cartesian coordinates will be optimised for   79 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -295.4099592     RMS force=    0.9280212455E-06
 OPTIM> Final energy  =    -286.9159099     RMS force=    0.8606920964E-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=     801.93    
 decide> The unconnected minima in the chain and their distances are:
     2        9.29     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 118 RMS= 20.5785 Dev= 39.79% S= 17.28 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=   1.84

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     536 steps. Energy=    -289.7575712       time=       0.42
 Minus side of path:                     591 steps. Energy=    -290.5710724       time=       0.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.7575712  1.2096         -288.5479422  2.0231         -290.5710724  11.401  10.381   2.353  33.572
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1603.9    
 decide> The unconnected minima in the chain and their distances are:
     2        9.29     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 2_F using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 735 RMS= 0.6081 Dev= 1.08% S= 18.67 time= 8.54
 Following    2 images are candidates for TS:   12   18  
 Converged to TS (number of iterations):         74
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=   1.95

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     717 steps. Energy=    -290.6361311       time=       0.62
 Minus side of path:                     570 steps. Energy=    -289.9345942       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6361311  5.6589         -284.9771962  4.9574         -289.9345942  22.167  20.816   1.798  43.944
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     616 steps. Energy=    -286.9159099       time=       0.53
 Minus side of path:                     554 steps. Energy=    -290.5717434       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -286.9159099  1.2595         -285.6564577  4.9153         -290.5717434  13.184   6.880  11.577   6.824
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1157.2    
 decide> The unconnected minima in the chain and their distances are:
     7       10.50     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 140 RMS= 17.8463 Dev= 16.68% S= 29.00 time= 0.24
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   1.31

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     619 steps. Energy=    -290.5717434       time=       0.53
 Minus side of path:                     544 steps. Energy=    -286.0397522       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5717434  4.8866         -285.6851371 0.35462         -286.0397522  14.838  13.507   1.952  40.473
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1214.0    
 decide> The unconnected minima in the chain and their distances are:
     8        8.95     5     6        7.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4423 Dev= 0.31% S= 9.05 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   0.81

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     574 steps. Energy=    -290.6361311       time=       0.45
 Minus side of path:                     530 steps. Energy=    -286.0397522       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6361311  4.6494         -285.9867606 0.52992E-01     -286.0397522   9.224   8.959   4.720  16.738
        Known (#5)                                              Known (#8)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 4.0873 Dev= 24.44% S= 9.61 time= 0.08
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=   5.24
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     994.14    
 decide> The unconnected minima in the chain and their distances are:
     6        7.92     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 6_F using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 630 RMS= 5.9955 Dev= 4.95% S= 11.98 time= 6.24
 Following    4 images are candidates for TS:    2    5    7   13  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         62
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):         16
 DNEB run yielded 4 true transition state(s) time=   3.28
 isnewts> transition state is the same as number        7 energy=     -295.8280775374
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     482 steps. Energy=    -295.4099592       time=       0.38
 Minus side of path:                     479 steps. Energy=    -297.6821932       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4099592 0.36322         -295.0467434  2.6354         -297.6821932   5.279   4.284   7.383  10.700
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     473 steps. Energy=    -297.6821932       time=       0.37
 Minus side of path:                     479 steps. Energy=    -297.2080073       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.6821932  1.8541         -295.8280775  1.3799         -297.2080073   5.038   4.821   2.506  31.527
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     475 steps. Energy=    -297.6821932       time=       0.37
 Minus side of path:                     567 steps. Energy=    -297.2080073       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.6821932  1.8541         -295.8280775  1.3799         -297.2080073  12.423  10.690   2.155  36.663
        Known (#9)                                              Known (#10)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     513 steps. Energy=    -289.9345942       time=       0.41
 Minus side of path:                     516 steps. Energy=    -297.6821932       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.9345942 0.32061         -289.6139801  8.0682         -297.6821932   8.982   6.933  10.738   7.357
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -295.4099592 0.36322        -295.0467434  2.6354        -297.6821932   5.279   4.284   7.383  10.700
   9     -297.6821932  8.0682        -289.6139801 0.32061        -289.9345942   8.982   6.933  10.738   7.357
   2     -289.9345942  4.9574        -284.9771962  5.6589        -290.6361311  22.167  20.816   1.798  43.944
   5     -290.6361311  4.6494        -285.9867606 0.52992E-01    -286.0397522   9.224   8.959   4.720  16.738
   4     -286.0397522 0.35462        -285.6851371  4.8866        -290.5717434  14.838  13.507   1.952  40.473
   3     -290.5717434  4.9153        -285.6564577  1.2595        -286.9159099  13.184   6.880  11.577   6.824

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                                38.16
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             44786 time=          23.25 %= 60.9
 OPTIM> # of energy+gradient+Hessian calls=       714 time=           0.77 %=  2.0
