
________________________________________________________________________________

___________________ CCP-EM Process | Refmac FSC (HM1 vs HM2) ___________________

__ Command _____________________________________________________________________
/Applications/ccp4-7.0/bin/refmac5 mapin1 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc mapin2 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc mapref /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc  << eof

mode sfcalc
sfcalc fsc
RESO 4.5
end
eof
________________________________________________________________________________
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<hr>
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<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
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 ### CCP4 7.0.067: Refmac          version 5.8.0238 : 10/15/18##
 ###############################################################
 User: tom  Run date: 12/ 2/2019 Run time: 11:14:52 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- mode sfcalc
  Data line--- sfcalc fsc
  Data line--- RESO 4.5
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - XYZIN
Output coordinate file. Logical name - XYZOUT actual file name - XYZOUT

  Refinement type                        : Idealisation
  Refinement type                        : NONE
  SF calculation from MAP: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /Applications/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /Applications/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically




Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 
   Current auto weighting coefficient =    13.74990    
 

 Logical Name: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc   Filename: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc 

File name for input map file on unit  10 : /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc
file size 501024 ; logical name /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc



           Number of columns, rows, sections ...............   50   50   50
           Map mode ........................................    2
           Start and stop points on columns, rows, sections    -7   42    5   54   -7   42
           Grid sampling on x, y, z ........................   50   50   50
           Cell dimensions .................................   75.0000    75.0000    75.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................     1.48683
           Mean density ....................................     0.02584
           Rms deviation from mean density .................     0.12309
           Space-group .....................................    0
           Number of titles ................................    1


     Labels:                            
  Created by TEMpy on: 2015-12-16


 res max nominal    3.000000      res max used    4.499959    
 mode : SFCA
 Map manupilation mode = M
 reference map
 
  Reference structure factors will be calculated from the map: 
 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4
 -5A.mrc

 Logical Name: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc   Filename: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc 

File name for input map file on unit  10 : /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc
file size 501024 ; logical name /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc



           Number of columns, rows, sections ...............   50   50   50
           Map mode ........................................    2
           Start and stop points on columns, rows, sections    -7   42    5   54   -7   42
           Grid sampling on x, y, z ........................   50   50   50
           Cell dimensions .................................   75.0000    75.0000    75.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................     1.48683
           Mean density ....................................     0.02584
           Rms deviation from mean density .................     0.12309
           Space-group .....................................    0
           Number of titles ................................    1


     Labels:                            
  Created by TEMpy on: 2015-12-16


          -7           5          -7          42          54          42
          -7           5          -7          42          54          42
          50          50          50           1           2           3
          50          50          50          -7           5          -7
          42          54          42
 Start reading           -7           5          -7          42          54
          42
           1
 
 Centre of gravity of the map =    17.0909820798943        30.2424981605501     
   16.6547719860745     
 Covariance of the map:
   40.5525719120672       -3.98157591536039        4.49597878823676     
  -3.98157614318245        34.6476830954972       -4.23890251270950     
   4.49597887981946       -4.23890220403956        48.7723872030351     
 Eigenvalues =   32.4022552491045        39.1025708751497     
   52.4678160863454     
 Eigenvectors:
  0.373840310087854       0.917624816718068       0.134937460686600     
 -0.825645023686425       0.262966103675822       0.499158414913942     
  0.422556170722023      -0.298015979539164       0.855939693275205     
 
 After map_reader_0           50          50          50           1           1
 Starting reso   0.1111121       4.499959    
 RelVol    3.375000    
 Number of resolution bins           21
 
  The number of bins for reference SF :          21

 Logical Name: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc   Filename: /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc 

File name for input map file on unit  10 : /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc
file size 501024 ; logical name /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4-5A.mrc



           Number of columns, rows, sections ...............   50   50   50
           Map mode ........................................    2
           Start and stop points on columns, rows, sections    -7   42    5   54   -7   42
           Grid sampling on x, y, z ........................   50   50   50
           Cell dimensions .................................   75.0000    75.0000    75.0000    90.0000    90.0000    90.0000
           Fast, medium, slow axes .........................    X    Y    Z
           Minimum density .................................     0.00000
           Maximum density .................................     1.48683
           Mean density ....................................     0.02584
           Rms deviation from mean density .................     0.12309
           Space-group .....................................    0
           Number of titles ................................    1


     Labels:                            
  Created by TEMpy on: 2015-12-16


 Starting (nominal) resolution   0.1111121       4.499959    
 Number of all maps for SF calculation :           2
 Map file number 1 
 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4
 -5A.mrc
 File number            1 
 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4
 -5A.mrc
          -7           5          -7          42          54          42
          -7           5          -7          42          54          42
          50          50          50           1           2           3
          50          50          50          -7           5          -7
          42          54          42
 Start reading           -7           5          -7          42          54
          42
           1
 
 Centre of gravity of the map =    17.0909820798943        30.2424981605501     
   16.6547719860745     
 Covariance of the map:
   40.5525719120672       -3.98157591536039        4.49597878823676     
  -3.98157614318245        34.6476830954972       -4.23890251270950     
   4.49597887981946       -4.23890220403956        48.7723872030351     
 Eigenvalues =   32.4022552491045        39.1025708751497     
   52.4678160863454     
 Eigenvectors:
  0.373840310087854       0.917624816718068       0.134937460686600     
 -0.825645023686425       0.262966103675822       0.499158414913942     
  0.422556170722023      -0.298015979539164       0.855939693275205     
 
 logname : MAPIN2 file name: 
 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4
 -5A.mrc
 File number            2 
 /Users/tom/code/devtools/checkout/ccpem/src/ccpem_core/test_data/map/mrc/1ake_4
 -5A.mrc
          -7           5          -7          42          54          42
          -7           5          -7          42          54          42
          50          50          50           1           2           3
          50          50          50          -7           5          -7
          42          54          42
 Start reading           -7           5          -7          42          54
          42
           1
 
 Centre of gravity of the map =    17.0909820798943        30.2424981605501     
   16.6547719860745     
 Covariance of the map:
   40.5525719120672       -3.98157591536039        4.49597878823676     
  -3.98157614318245        34.6476830954972       -4.23890251270950     
   4.49597887981946       -4.23890220403956        48.7723872030351     
 Eigenvalues =   32.4022552491045        39.1025708751497     
   52.4678160863454     
 Eigenvectors:
  0.373840310087854       0.917624816718068       0.134937460686600     
 -0.825645023686425       0.262966103675822       0.499158414913942     
  0.422556170722023      -0.298015979539164       0.855939693275205     
 
 logname : MAPIN3 file name: 
 Number of maps            2
 Calculating Fourier coefficients for the map number            1
 Calculating Fourier coefficients for the map number            2
 Number of resolution bins           21

    ****         FSC and other statistics: Without accounting for mask          ****

 $TABLE: FSC and other statistics
 $GRAPHS: FSC cos(deltaPHI), cor(|F1|,|F2|) vs resolutions: 1,5,6,8,12
 $$
 2sin(th)/l 2sin(th)/l NREF sigma  FSC FSCT PHdiff cos(PHdiff) sigmaSig ZZ TT cor(|F1|,|F2|) $$  $$
  1.7777777E-04  2.5142860E-03         125  4.0000002E-03   1.000000    
  0.9999993      0.0000000E+00   1.000000       374726.6     NaN           
 NaN              1.000000    
  2.5142860E-03  4.8507941E-03         184  2.5475543E-04  0.9999999    
  0.9999999      0.0000000E+00   1.000000       31389.09       116.5668    
   39073.35      0.9999996    
  4.8507941E-03  7.1873022E-03         213 -4.5848005E-06   1.000000    
   1.000000      0.0000000E+00   1.000000       21454.01     Infinity      
 Infinity        0.9999999    
  7.1873022E-03  9.5238108E-03         301  1.0382060E-04   1.000000    
   1.000000      0.0000000E+00   1.000000       15826.81     Infinity      
 Infinity         1.000000    
  9.5238108E-03  1.1860318E-02         327  5.9728595E-06  0.9999999    
   1.000000      0.0000000E+00   1.000000       10528.08       155.9581    
   52213.96      0.9999997    
  1.1860318E-02  1.4196826E-02         322 -2.5778823E-05   1.000000    
   1.000001      0.0000000E+00   1.000000       7701.959     NaN           
 NaN              1.000001    
  1.4196826E-02  1.6533334E-02         417 -2.6931581E-05   1.000000    
  0.9999995      0.0000000E+00   1.000000       5694.396     Infinity      
 Infinity         1.000000    
  1.6533334E-02  1.8869841E-02         423  0.0000000E+00  0.9999999    
   1.000000      0.0000000E+00   1.000000       4438.999       177.5661    
   59427.30      0.9999998    
  1.8869841E-02  2.1206349E-02         412  7.1108921E-06   1.000000    
  0.9999990      0.0000000E+00   1.000000       4113.946     NaN           
 NaN              1.000000    
  2.1206349E-02  2.3542857E-02         477  2.0473008E-06   1.000000    
   1.000001      0.0000000E+00   1.000000       3419.815     NaN           
 NaN              1.000000    
  2.3542857E-02  2.5879364E-02         423  0.0000000E+00  0.9999999    
   1.000001      0.0000000E+00   1.000000       2990.518       170.4635    
   42021.44      0.9999998    
  2.5879364E-02  2.8215872E-02         568 -3.8684252E-06   1.000000    
  0.9999993      0.0000000E+00   1.000000       2600.004     Infinity      
 Infinity        0.9999996    
  2.8215872E-02  3.0552380E-02         525  1.4880952E-05   1.000000    
   1.000000      0.0000000E+00   1.000000       2747.029     NaN           
 NaN              1.000000    
  3.0552380E-02  3.2888889E-02         576 -3.3908420E-06   1.000000    
   1.000001      0.0000000E+00   1.000000       2819.552     Infinity      
 Infinity        0.9999998    
  3.2888889E-02  3.5225399E-02         583  1.0050386E-05   1.000000    
   1.000000      0.0000000E+00   1.000000       2732.589     NaN           
 NaN              1.000000    
  3.5225399E-02  3.7561908E-02         606 -3.2229786E-06   1.000000    
  0.9999993      0.0000000E+00   1.000000       2907.416     NaN           
 NaN              1.000000    
  3.7561908E-02  3.9898418E-02         516  5.6776889E-06   1.000000    
   1.000001      0.0000000E+00   1.000000       2799.771     NaN           
 NaN              1.000001    
  3.9898418E-02  4.2234927E-02         711  2.7470112E-06   1.000000    
  0.9999994      0.0000000E+00   1.000000       2846.691     NaN           
 NaN              1.000000    
  4.2234927E-02  4.4571437E-02         622 -9.4202169E-06   1.000000    
  0.9999996      0.0000000E+00   1.000000       2977.361     NaN           
 NaN              1.000000    
  4.4571437E-02  4.6907946E-02         591 -5.3702674E-06  0.9999999    
   1.000002      0.0000000E+00   1.000000       2783.471       210.0991    
   70291.46       1.000000    
  4.6907946E-02  4.9244467E-02         768  0.0000000E+00  0.9999999    
   1.000001      0.0000000E+00   1.000000       2760.464       230.0581    
   56681.88      0.9999991    
 $$
 After fsc_sigma  T F
          21          21          21   1.000000    
 resolution limit           21   4.506312              21   4.506312    
 Starting B value for sharpening    5.489890    
 
 Structure factors will be sharpened using reference map/curveR 
 
   Map maximum =    3.210803    
   Map minimum =  -0.8872576    
   Map mean    =   4.8461914E-08
   Map rmsd    =   0.3696143    
 
 Print stats of the original data to the file: orig_data_rescut.txt
 Number of resolution bins           21

    ****      Mean(|F|) and other statistics: Without accounting for mask       ****

 $TABLE: Mean(|F|) and other statistics
 $GRAPHS: Mean(|F|), Mean(|F|^2), Mean(|F|^4) vs resolutions: 1,6,7,8
 $$
2sin(th)/l 2sin(th)/l dmin dmax NREF Mn(|F|) Mn(|F|^2) Mn(|F|^4) Mn(A) Mn(B) Mn(A^2) Mn(B^2) cor(A,B) $$
 $$
0.000 0.003  75.00  19.94   125  0.13826E+04  0.42684E+07  0.13721E+15 -0.29763E+02  0.18775E+02  0.19927E+07  0.22757E+07 -0.067
0.003 0.005  19.94  14.36   184  0.52846E+03  0.35754E+06  0.27319E+12  0.89211E-01 -0.41555E+01  0.17449E+06  0.18305E+06 -0.049
0.005 0.007  14.36  11.80   213  0.42848E+03  0.24437E+06  0.13303E+12  0.16365E+02  0.16769E+02  0.13375E+06  0.11062E+06 -0.063
0.007 0.010  11.80  10.25   301  0.37192E+03  0.18028E+06  0.69642E+11 -0.15854E+02 -0.88515E+01  0.90955E+05  0.89323E+05  0.051
0.010 0.012  10.25   9.18   327  0.30513E+03  0.11992E+06  0.29405E+11  0.43817E+01  0.26344E+01  0.63181E+05  0.56741E+05 -0.074
0.012 0.014   9.18   8.39   322  0.26005E+03  0.87730E+05  0.15867E+11 -0.67550E+01  0.46445E+01  0.42057E+05  0.45674E+05 -0.104
0.014 0.017   8.39   7.78   417  0.22508E+03  0.64863E+05  0.90445E+10  0.77678E+00  0.12143E+00  0.32590E+05  0.32273E+05  0.028
0.017 0.019   7.78   7.28   423  0.19919E+03  0.50563E+05  0.50406E+10 -0.46256E+00 -0.31868E+00  0.25465E+05  0.25098E+05 -0.055
0.019 0.021   7.28   6.87   412  0.19215E+03  0.46860E+05  0.42973E+10 -0.16097E+01 -0.12166E+02  0.23017E+05  0.23844E+05 -0.051
0.021 0.024   6.87   6.52   477  0.17421E+03  0.38954E+05  0.31079E+10  0.54502E+01  0.10031E+02  0.19631E+05  0.19323E+05  0.040
0.024 0.026   6.52   6.22   423  0.16245E+03  0.34064E+05  0.24960E+10 -0.26639E+01  0.50724E+00  0.18461E+05  0.15603E+05 -0.013
0.026 0.028   6.22   5.95   568  0.15197E+03  0.29616E+05  0.17730E+10 -0.21086E+00 -0.65601E+01  0.14837E+05  0.14778E+05 -0.079
0.028 0.031   5.95   5.72   525  0.15696E+03  0.31290E+05  0.19974E+10 -0.48617E-01  0.60218E+01  0.14744E+05  0.16546E+05  0.000
0.031 0.033   5.72   5.51   576  0.15807E+03  0.32116E+05  0.21351E+10 -0.14195E+01  0.49847E+01  0.15049E+05  0.17067E+05  0.008
0.033 0.035   5.51   5.33   583  0.15491E+03  0.31126E+05  0.20506E+10 -0.55777E+01 -0.88281E+01  0.15278E+05  0.15848E+05 -0.015
0.035 0.038   5.33   5.16   606  0.16043E+03  0.33117E+05  0.22910E+10  0.94789E+01 -0.14136E+01  0.16761E+05  0.16356E+05  0.054
0.038 0.040   5.16   5.01   516  0.15975E+03  0.31891E+05  0.19183E+10 -0.39295E+00  0.49946E+01  0.16140E+05  0.15752E+05  0.051
0.040 0.042   5.01   4.87   711  0.15975E+03  0.32426E+05  0.20666E+10  0.62662E-01  0.84547E+01  0.15676E+05  0.16750E+05 -0.039
0.042 0.045   4.87   4.74   622  0.16264E+03  0.33914E+05  0.23415E+10 -0.10238E+02 -0.13377E+02  0.16583E+05  0.17331E+05  0.051
0.045 0.047   4.74   4.62   591  0.15725E+03  0.31705E+05  0.20226E+10  0.11994E+02  0.58351E+01  0.16893E+05  0.14812E+05  0.073
0.047 0.049   4.62   4.51   768  0.15820E+03  0.31443E+05  0.18903E+10 -0.21752E+01 -0.21172E+01  0.15743E+05  0.15700E+05 -0.001
 $$
 sharpening things:            7           4   5.489890       1.829963    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: starting_map.mtz   Filename: starting_map.mtz 

  Crd file =   F
  Time in seconds: CPU =         0.09
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
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 Refmac:  End of Refmac_5.8.0238  
Times: User:       0.1s System:    0.0s Elapsed:     0:01  
</pre>
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CCP-EM version dev 1.2.0-23-g7721cb7 ___________________________________________

CCP-EM process finished Tuesday, 12. February 2019 11:14am _____________________
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