
 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)@comp32.ch.
                 Created on  5/28/12 at 12:16:39 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


 natintsetup, NATOMS           79
 cartres            7
 KeyInt>> Using natural internal coordinates. # of coords =        231
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         44      2388
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -296.4813651     RMS force=    0.9136900815E-06
 OPTIM> Final energy  =    -291.8670829     RMS force=    0.8319218038E-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=     860.44    
 decide> The unconnected minima in the chain and their distances are:
     2        9.51     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.1948 Dev= 1.00% S= 11.35 time= 0.12
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   0.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     575 steps. Energy=    -295.7886632       time=       0.51
 Minus side of path:                     465 steps. Energy=    -293.2739393       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.7886632  3.0740         -292.7147052 0.55923         -293.2739393   7.646   6.056   7.225  10.935
        *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      3 steps with      2 missing connections, weight=     1584.9    
 decide> The unconnected minima in the chain and their distances are:
     2        9.46     4     3        9.04     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 1.0959 Dev= 1.32% S= 10.41 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   0.77

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     691 steps. Energy=    -294.6728481       time=       0.70
 Minus side of path:                     635 steps. Energy=    -295.7886632       time=       0.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.6728481  5.0537         -289.6191768  6.1695         -295.7886632  14.165   6.851  12.931   6.109
        *NEW* (Placed in 5)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9760 Dev= 0.96% S= 10.07 time= 0.12
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.76

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     487 steps. Energy=    -296.4813651       time=       0.41
 Minus side of path:                     461 steps. Energy=    -297.0490762       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.4813651  3.5062         -292.9751666  4.0739         -297.0490762   6.531   5.301   8.201   9.633
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     807.59    
 decide> The unconnected minima in the chain and their distances are:
     2        7.70     5     3        7.05     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.3988 Dev= 0.11% S= 8.61 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   1.02

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     473 steps. Energy=    -290.7876332       time=       0.39
 Minus side of path:                     485 steps. Energy=    -291.8670829       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.7876332 0.61907         -290.1685674  1.6985         -291.8670829   7.215   6.317   6.596  11.977
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.7294 Dev= 0.60% S= 8.07 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   0.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     517 steps. Energy=    -295.7886632       time=       0.43
 Minus side of path:                     486 steps. Energy=    -297.0490762       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.7886632  2.1744         -293.6142847  3.4348         -297.0490762  11.201   7.067  16.965   4.657
        Known (#3)                                              Known (#6)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     140.11    
 decide> The unconnected minima in the chain and their distances are:
     7        5.19     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3941 Dev= 0.92% S= 5.62 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.57

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     435 steps. Energy=    -290.7876332       time=       0.35
 Minus side of path:                     475 steps. Energy=    -291.0412270       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.7876332 0.56816E-01     -290.7308171 0.31041         -291.0412270   4.704   4.531  12.953   6.099
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     19.208    
 decide> The unconnected minima in the chain and their distances are:
     8        2.68     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4243 Dev= 3.29% S= 3.04 time= 0.11
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   0.83

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     475 steps. Energy=    -289.6130578       time=       0.39
 Minus side of path:                     477 steps. Energy=    -291.0412270       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.6130578 0.40489         -289.2081638  1.8331         -291.0412270   4.566   4.317  14.696   5.376
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     38.416    
 decide> The unconnected minima in the chain and their distances are:
     8        2.68     5 
 

 tryconnect> 210-iteration DNEB run for minima 5_S and 8_F using 6 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      29.25260720    
 Double-ended search iterations= 210 RMS= 0.5313 Dev= 4.83% S= 3.15 time= 0.79
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.61

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     505 steps. Energy=    -294.6728481       time=       0.43
 Minus side of path:                     460 steps. Energy=    -290.7876332       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.6728481  5.4440         -289.2288309  1.5588         -290.7876332   5.877   5.195   9.420   8.387
        Known (#5)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -296.4813651  3.5062        -292.9751666  4.0739        -297.0490762   6.531   5.301   8.201   9.633
   5     -297.0490762  3.4348        -293.6142847  2.1744        -295.7886632  11.201   7.067  16.965   4.657
   2     -295.7886632  6.1695        -289.6191768  5.0537        -294.6728481  14.165   6.851  12.931   6.109
   8     -294.6728481  5.4440        -289.2288309  1.5588        -290.7876332   5.877   5.195   9.420   8.387
   4     -290.7876332 0.61907        -290.1685674  1.6985        -291.8670829   7.215   6.317   6.596  11.977

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

 Elapsed time=                                15.03
 OPTIM> # of energy calls=                         40 time=           0.02 %=  0.2
 OPTIM> # of energy+gradient calls=             14548 time=           8.21 %= 54.6
 OPTIM> # of energy+gradient+Hessian calls=       257 time=           0.28 %=  1.9
