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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 12:00:58 


 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.


 $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--- make     check NONE
  Data line--- refi     type REST reso 42.68 1.15     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 11
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: EP_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FREE

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


Input coordinate file.  Logical name - XYZIN actual file name  - EP_R00_1-20A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - EP_R00_1-15A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - EP_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - EP_R00_1-15A.mtz

Cell from mtz :    45.203    73.097    52.573    90.000   109.248    90.000
Space group from mtz: number -    4; name - P 1 21 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    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


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    11       0.0687
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    42.6836  1.1500
  Estimated number of reflections :     164864
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    42.6836  1.1500

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

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
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :EP_R00_1-20A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    2459
  Number of residues :     330
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:CE   LYS                63  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS                63  AAA  is missing in the structure
  ATTENTION: atom:CD   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS               110  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               110  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               142  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               149  AAA  is missing in the structure
  ATTENTION: atom:CG   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:CD   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               243  AAA  is missing in the structure
  ATTENTION: atom:OXT  ALA               328  AAA  is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :     330
  Number of atoms                   :    4853
  Number of missing atoms           :       7
  Number of rebuilt atoms           :    2344
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0317


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      4719         0      4719
               Angles:      8613         0      8613
              Chirals:       376         0       376
               Planes:       786         0       786
             Torsions:      2619         0      2619
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections       5767
Number of   all  reflections     114320
--------------------------------------------------------------------------------
 Number of reflections in file     149916
 Number of reflections read         114320

   Current auto weighting coefficient =    5.3747091    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.892 id.= 2.950 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   128  210  150
 Maximuum H,K,L                 :    40   64   46
 Minimum acceptable grid spacing:    85  137   99
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   128  210  150
 Maximuum H,K,L                 :    40   64   46
 Minimum acceptable grid spacing:    85  137   99
 Weight matrix   0.22189483    
 Actual weight    5.3747091      is applied to the X-ray term
Norm of X_ray positional gradient                73.7
Norm of Geom. positional gradient                98.9
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                 0.161E+04
Product of X_ray and Geom posit. gradients     -0.504E+08
 Cosine of angle between them                      -0.496
Product of X_ray and Geom B-fact gradients     -0.206E+08
 Cosine of angle between them                      -0.006


Residuals: XRAY=     0.2374E+07 GEOM=     0.2330E+05 TOTAL=     0.2397E+07
 function value    2397374.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.038     0.017
Bond angles  : refined atoms                   3498     1.793     1.637
Bond angles  : others                          5115     2.544     1.563
Torsion angles, period  1. refined              363     6.970     5.000
Torsion angles, period  2. refined               86    29.764    25.000
Torsion angles, period  3. refined              342    10.454    15.000
Torsion angles, period  4. refined                1    14.939    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.013     0.020
Planar groups: others                           524     0.024     0.020
VDW repulsions: refined_atoms                   432     0.240     0.200
VDW repulsions.others                          1916     0.228     0.200
VDW; torsion: refined_atoms                    1289     0.173     0.200
VDW; torsion.others                            1073     0.079     0.200
HBOND: refined_atoms                             36     0.124     0.200
VDW repulsions: symmetry: refined_atoms           2     0.082     0.200
VDW repulsions: symmetry: others                 26     0.145     0.200
HBOND: symmetry: refined_atoms                    3     0.022     0.200
M. chain bond B values: refined atoms          1369     1.770     1.317
M. chain bond B values: others                 1368     1.772  8292.663
M. chain angle B values: refined atoms         1719     2.065     1.995
M. chain angle B values: others                1720     2.065    11.002
S. chain bond B values: refined atoms          1164     2.229     1.438
S. chain bond B values: others                 1164     2.229**********
S. chain angle B values: refined atoms         1765     2.501     2.103
S. chain angle B values: others                1765     2.501     2.102
Long range B values: refined atoms             2679     2.493    15.895
Long range B values: others                    2680     2.493    20.511
Rigid bond restraints                          2533     7.613     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0485, B  =   -0.4714
Partial structure    1: scale =     0.5067, B  =   39.4322
Overall anisotropic scale factors
   B11 =   1.15 B22 =  -0.03 B33 =  -0.25 B12 =   0.00 B13 =  -1.16 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    3069  99.54   286.0   293.5  0.21  0.23     162   275.6   292.8  0.22  0.23
 0.104    5461  99.31   207.7   193.0  0.21  0.21     290   201.3   189.4  0.26  0.25
 0.172    6998  98.79   124.4   121.7  0.21  0.20     365   124.5   125.7  0.27  0.25
 0.241    8226  98.38    96.6    91.1  0.19  0.18     434    92.3    88.6  0.26  0.23
 0.310    9284  97.93    59.7    56.3  0.18  0.16     489    61.1    57.6  0.24  0.22
 0.378   10168  97.35    41.3    38.6  0.20  0.18     533    42.3    39.7  0.27  0.26
 0.447   10969  96.45    31.9    29.0  0.24  0.23     576    32.0    28.9  0.29  0.29
 0.516   11666  96.05    24.8    22.6  0.29  0.29     626    25.5    23.0  0.30  0.30
 0.584   12407  95.38    20.1    18.2  0.35  0.36     650    19.9    18.3  0.37  0.37
 0.653   12971  94.82    17.1    15.2  0.38  0.38     699    17.2    15.2  0.37  0.37
 0.722   13492  94.03    14.5    13.0  0.43  0.44     754    14.6    12.7  0.43  0.45
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0349   2851   0.873    218   0.763   3069   0.865  0.937  0.9405  0.9486  0.8819  0.8609
  0.1036   5232   0.845    229   0.741   5461   0.841  1.003  0.9154  0.9327  0.8444  0.8897
  0.1723   6783   0.810    215   0.709   6998   0.806  0.969  0.9139  0.9251  0.8154  0.8836
  0.2410   7998   0.822    228   0.674   8226   0.817  0.999  0.9108  0.9335  0.8308  0.9038
  0.3097   9059   0.800    225   0.719   9284   0.798  0.975  0.9153  0.9331  0.8499  0.9212
  0.3783   9941   0.730    227   0.659  10168   0.728  0.932  0.8834  0.9067  0.7895  0.8965
  0.4470  10735   0.655    234   0.596  10969   0.654  0.898  0.8446  0.8705  0.7420  0.8513
  0.5157  11438   0.604    228   0.555  11666   0.603  0.806  0.8136  0.8197  0.7043  0.7401
  0.5844  12169   0.451    238   0.394  12407   0.450  0.665  0.7088  0.7190  0.4983  0.6083
  0.6531  12750   0.408    221   0.386  12971   0.408  0.614  0.6732  0.6819  0.4987  0.4772
  0.7218  13295   0.322    224   0.300  13519   0.321  0.519  0.5915  0.5927  0.3513  0.2722
 $$
Resolution limits                    =     42.684     1.150
Number of used reflections           =     104738
Percentage observed                  =    96.4985
Percentage of free reflections       =     5.0581
Overall R factor                     =     0.2306
Free R factor                        =     0.2714
Average Fourier shell correlation    =     0.8109
AverageFree Fourier shell correlation=     0.7956
Overall weighted R factor            =     0.2194
Free weighted R factor               =     0.2571
Overall weighted R2 factor           =     0.2904
Free weighted R2 factor              =     0.2809
Average correlation coefficient      =     0.7083
Overall correlation coefficient      =     0.9533
Free correlation coefficient         =     0.9415
Cruickshanks DPI for coordinate error=     0.0471
DPI based on free R factor           =     0.0492
Overall figure of merit              =     0.6096
ML based su of positional parameters =     0.0683
ML based su of thermal parameters    =     3.7320
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    441711.81       23301.902       2397374.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.20170262    
 Actual weight    5.3747091      is applied to the X-ray term


 function value    2448095.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.019     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0483, B  =   -0.8406
Partial structure    1: scale =     0.5084, B  =   39.7924
Overall anisotropic scale factors
   B11 =   1.40 B22 =  -0.05 B33 =  -0.37 B12 =   0.00 B13 =  -1.26 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2311
Free R factor                        =     0.2710
Average Fourier shell correlation    =     0.8171
AverageFree Fourier shell correlation=     0.7989
Average correlation coefficient      =     0.7101
Overall figure of merit              =     0.5851
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02


 fvalues    453650.72       17173.592       2495550.8       2397374.5    

 fvalues    453650.72       17173.592       2467780.0       2455414.3    
 fvalues    453650.72       17173.592       2467780.0       2455414.3    


     CGMAT cycle number =      3

 Weight matrix   0.17849056    
 Actual weight    4.8860993      is applied to the X-ray term


 function value    2240301.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.017     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0483, B  =   -0.9213
Partial structure    1: scale =     0.5091, B  =   39.8578
Overall anisotropic scale factors
   B11 =   1.45 B22 =  -0.06 B33 =  -0.40 B12 =   0.00 B13 =  -1.27 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2313
Free R factor                        =     0.2709
Average Fourier shell correlation    =     0.8166
AverageFree Fourier shell correlation=     0.7984
Average correlation coefficient      =     0.7097
Overall figure of merit              =     0.5778
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    455062.78       16819.381       2240301.5       2455414.3    


     CGMAT cycle number =      4

 Weight matrix   0.15974171    
 Actual weight    4.4419084      is applied to the X-ray term


 function value    2046942.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.013     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -1.0467
Partial structure    1: scale =     0.5094, B  =   40.0081
Overall anisotropic scale factors
   B11 =   1.54 B22 =  -0.07 B33 =  -0.45 B12 =   0.00 B13 =  -1.30 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2318
Free R factor                        =     0.2710
Average Fourier shell correlation    =     0.8222
AverageFree Fourier shell correlation=     0.8044
Average correlation coefficient      =     0.7089
Overall figure of merit              =     0.5763
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    457090.75       16587.100       2046942.4       2240301.5    


     CGMAT cycle number =      5

 Weight matrix   0.14183511    
 Actual weight    4.0380983      is applied to the X-ray term


 function value    1873630.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.011     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -1.1796
Partial structure    1: scale =     0.5092, B  =   40.0986
Overall anisotropic scale factors
   B11 =   1.62 B22 =  -0.08 B33 =  -0.50 B12 =   0.00 B13 =  -1.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2324
Free R factor                        =     0.2710
Average Fourier shell correlation    =     0.8247
AverageFree Fourier shell correlation=     0.8068
Average correlation coefficient      =     0.7080
Overall figure of merit              =     0.5718
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    459875.59       16607.773       1873630.6       2046942.4    


     CGMAT cycle number =      6

 Weight matrix   0.14093266    
 Actual weight    4.0380983      is applied to the X-ray term


 function value    1879806.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -1.3182
Partial structure    1: scale =     0.5090, B  =   40.2014
Overall anisotropic scale factors
   B11 =   1.70 B22 =  -0.09 B33 =  -0.54 B12 =   0.00 B13 =  -1.34 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2331
Free R factor                        =     0.2710
Average Fourier shell correlation    =     0.8297
AverageFree Fourier shell correlation=     0.8116
Average correlation coefficient      =     0.7067
Overall figure of merit              =     0.5728
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    461644.09       16492.164       1887608.4       1873630.6    

 fvalues    461644.09       16492.164       1885825.5       1880656.4    
 fvalues    461644.09       16492.164       1885825.5       1880656.4    


     CGMAT cycle number =      7

 Weight matrix   0.14108254    
 Actual weight    4.0380983      is applied to the X-ray term


 function value    1880191.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -1.3486
Partial structure    1: scale =     0.5090, B  =   40.2529
Overall anisotropic scale factors
   B11 =   1.71 B22 =  -0.09 B33 =  -0.55 B12 =   0.00 B13 =  -1.34 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2332
Free R factor                        =     0.2710
Average Fourier shell correlation    =     0.8316
AverageFree Fourier shell correlation=     0.8132
Average correlation coefficient      =     0.7065
Overall figure of merit              =     0.5735
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    461532.63       16477.158       1880191.3       1880656.4    


     CGMAT cycle number =      8

 Weight matrix   0.13908839    
 Actual weight    4.0380983      is applied to the X-ray term


 function value    1886229.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.007     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -1.4025
Partial structure    1: scale =     0.5093, B  =   40.3433
Overall anisotropic scale factors
   B11 =   1.74 B22 =  -0.09 B33 =  -0.57 B12 =   0.00 B13 =  -1.35 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2335
Free R factor                        =     0.2712
Average Fourier shell correlation    =     0.8311
AverageFree Fourier shell correlation=     0.8127
Average correlation coefficient      =     0.7060
Overall figure of merit              =     0.5695
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    463108.09       16445.840       1890150.1       1880191.3    

 fvalues    463108.09       16445.840       1888176.3       1886521.9    
 fvalues    463108.09       16445.840       1888176.3       1886521.9    


     CGMAT cycle number =      9

 Weight matrix   0.13874666    
 Actual weight    4.0380983      is applied to the X-ray term


 function value    1887810.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.007     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0480, B  =   -1.4257
Partial structure    1: scale =     0.5089, B  =   40.3215
Overall anisotropic scale factors
   B11 =   1.75 B22 =  -0.09 B33 =  -0.57 B12 =   0.00 B13 =  -1.35 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2336
Free R factor                        =     0.2711
Average Fourier shell correlation    =     0.8312
AverageFree Fourier shell correlation=     0.8128
Average correlation coefficient      =     0.7059
Overall figure of merit              =     0.5691
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    463426.53       16449.736       1888896.3       1886521.9    

 fvalues    463426.53       16449.736       1888074.1       1887811.6    
 fvalues    463426.53       16449.736       1888074.1       1887811.6    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.984 id.= 2.950 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   128  210  150
 Maximuum H,K,L                 :    40   64   46
 Minimum acceptable grid spacing:    85  137   99
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   128  210  150
 Maximuum H,K,L                 :    40   64   46
 Minimum acceptable grid spacing:    85  137   99
 Weight matrix   0.13869250    
 Actual weight    4.0380983      is applied to the X-ray term
Norm of X_ray positional gradient                62.8
Norm of Geom. positional gradient                62.3
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  720.
Product of X_ray and Geom posit. gradients     -0.504E+08
 Cosine of angle between them                      -0.925
Product of X_ray and Geom B-fact gradients     -0.198E+07
 Cosine of angle between them                      -0.001


Residuals: XRAY=     0.1871E+07 GEOM=     0.1645E+05 TOTAL=     0.1888E+07
 function value    1887775.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.007     0.017
Bond angles  : refined atoms                   3498     1.869     1.637
Bond angles  : others                          5115     1.622     1.563
Torsion angles, period  1. refined              363     7.060     5.000
Torsion angles, period  2. refined               86    29.875    25.000
Torsion angles, period  3. refined              342    10.534    15.000
Torsion angles, period  4. refined                1    15.850    15.000
Chiral centres: refined atoms                   376     0.094     0.200
Planar groups: refined atoms                   2955     0.013     0.020
Planar groups: others                           524     0.005     0.020
VDW repulsions: refined_atoms                   434     0.239     0.200
VDW repulsions.others                          1913     0.205     0.200
VDW; torsion: refined_atoms                    1285     0.173     0.200
VDW; torsion.others                            1124     0.082     0.200
HBOND: refined_atoms                             39     0.120     0.200
VDW repulsions: symmetry: refined_atoms           2     0.090     0.200
VDW repulsions: symmetry: others                 26     0.144     0.200
HBOND: symmetry: refined_atoms                    2     0.031     0.200
M. chain bond B values: refined atoms          1369     1.690     1.339
M. chain bond B values: others                 1368     1.691  8714.693
M. chain angle B values: refined atoms         1719     1.956     2.030
M. chain angle B values: others                1720     1.956    11.470
S. chain bond B values: refined atoms          1164     2.092     1.462
S. chain bond B values: others                 1164     2.091**********
S. chain angle B values: refined atoms         1765     2.326     2.140
S. chain angle B values: others                1765     2.326     2.139
Long range B values: refined atoms             2680     2.325    16.141
Long range B values: others                    2681     2.326    16.141
Rigid bond restraints                          2533    14.995     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0480, B  =   -1.4213
Partial structure    1: scale =     0.5091, B  =   40.3466
Overall anisotropic scale factors
   B11 =   1.75 B22 =  -0.09 B33 =  -0.57 B12 =   0.00 B13 =  -1.35 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    3069  99.54   288.8   294.9  0.21  0.23     162   278.3   294.7  0.22  0.23
 0.104    5461  99.31   209.8   194.3  0.22  0.21     290   203.3   190.9  0.26  0.25
 0.172    6998  98.79   125.6   123.0  0.22  0.20     365   125.7   126.3  0.27  0.25
 0.241    8226  98.38    97.6    92.5  0.20  0.18     434    93.2    89.8  0.25  0.23
 0.310    9284  97.93    60.3    57.2  0.19  0.17     489    61.7    58.3  0.24  0.22
 0.378   10168  97.35    41.7    39.0  0.21  0.19     533    42.7    40.2  0.27  0.25
 0.447   10969  96.45    32.2    29.2  0.25  0.24     576    32.3    29.1  0.29  0.28
 0.516   11666  96.05    25.1    22.6  0.29  0.29     626    25.8    23.0  0.31  0.31
 0.584   12407  95.38    20.3    18.1  0.35  0.35     650    20.0    18.0  0.36  0.37
 0.653   12971  94.82    17.2    15.0  0.38  0.38     699    17.4    14.9  0.37  0.37
 0.722   13492  94.03    14.7    12.8  0.42  0.43     754    14.7    12.6  0.42  0.44
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0349   2851   0.889    218   0.792   3069   0.882  0.942  0.9449  0.9532  0.8803  0.8597
  0.1036   5232   0.844    229   0.743   5461   0.840  1.003  0.9165  0.9335  0.8429  0.8881
  0.1723   6783   0.809    215   0.714   6998   0.806  0.969  0.9177  0.9273  0.8168  0.8798
  0.2410   7998   0.815    228   0.689   8226   0.812  0.999  0.9156  0.9365  0.8355  0.9001
  0.3097   9059   0.777    225   0.710   9284   0.775  0.975  0.9172  0.9340  0.8516  0.9115
  0.3783   9941   0.682    227   0.627  10168   0.681  0.929  0.8878  0.9087  0.7931  0.8825
  0.4470  10735   0.591    234   0.565  10969   0.590  0.898  0.8584  0.8770  0.7572  0.8380
  0.5157  11438   0.510    228   0.490  11666   0.510  0.796  0.8151  0.8244  0.6937  0.7313
  0.5844  12169   0.385    238   0.356  12407   0.384  0.680  0.7311  0.7497  0.5038  0.6096
  0.6531  12750   0.317    221   0.331  12971   0.318  0.614  0.6792  0.7002  0.5033  0.4814
  0.7218  13295   0.336    224   0.326  13519   0.336  0.593  0.6717  0.6886  0.3534  0.2884
 $$
Resolution limits                    =     42.684     1.150
Number of used reflections           =     104738
Percentage observed                  =    96.4985
Percentage of free reflections       =     5.0581
Overall R factor                     =     0.2336
Free R factor                        =     0.2712
Average Fourier shell correlation    =     0.8312
AverageFree Fourier shell correlation=     0.8128
Overall weighted R factor            =     0.2217
Free weighted R factor               =     0.2569
Overall weighted R2 factor           =     0.2925
Free weighted R2 factor              =     0.2807
Average correlation coefficient      =     0.7058
Overall correlation coefficient      =     0.9524
Free correlation coefficient         =     0.9416
Cruickshanks DPI for coordinate error=     0.0477
DPI based on free R factor           =     0.0492
Overall figure of merit              =     0.5689
ML based su of positional parameters =     0.0748
ML based su of thermal parameters    =     4.1846
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    463416.94       16452.547       1887775.6       1887811.6    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.985 id.= 2.950 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FREE=FREE FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: EP_R00_1-15A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.007     0.017
Bond angles  : refined atoms                   3498     1.869     1.637
Bond angles  : others                          5115     1.621     1.563
Torsion angles, period  1. refined              363     7.061     5.000
Torsion angles, period  2. refined               86    29.876    25.000
Torsion angles, period  3. refined              342    10.535    15.000
Torsion angles, period  4. refined                1    15.873    15.000
Chiral centres: refined atoms                   376     0.094     0.200
Planar groups: refined atoms                   2955     0.013     0.020
Planar groups: others                           524     0.005     0.020
VDW repulsions: refined_atoms                   434     0.239     0.200
VDW repulsions.others                          1912     0.205     0.200
VDW; torsion: refined_atoms                    1285     0.173     0.200
VDW; torsion.others                            1122     0.083     0.200
HBOND: refined_atoms                             39     0.120     0.200
VDW repulsions: symmetry: refined_atoms           2     0.090     0.200
VDW repulsions: symmetry: others                 27     0.142     0.200
HBOND: symmetry: refined_atoms                    2     0.032     0.200
M. chain bond B values: refined atoms          1369     1.690     1.340
M. chain bond B values: others                 1368     1.691  8719.133
M. chain angle B values: refined atoms         1719     1.955     2.031
M. chain angle B values: others                1720     1.955    11.474
S. chain bond B values: refined atoms          1164     2.091     1.463
S. chain bond B values: others                 1164     2.090**********
S. chain angle B values: refined atoms         1765     2.325     2.140
S. chain angle B values: others                1765     2.324     2.139
Long range B values: refined atoms             2680     2.324    16.146
Long range B values: others                    2681     2.324    16.146
Rigid bond restraints                          2533    15.038     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0480, B  =   -1.4294
Partial structure    1: scale =     0.5091, B  =   40.3643
Overall anisotropic scale factors
   B11 =   1.75 B22 =  -0.10 B33 =  -0.58 B12 =   0.00 B13 =  -1.35 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    3069  99.54   288.9   294.9  0.21  0.23     162   278.3   294.8  0.22  0.23
 0.104    5461  99.31   209.8   194.3  0.22  0.21     290   203.3   190.9  0.26  0.25
 0.172    6998  98.79   125.6   123.0  0.22  0.20     365   125.7   126.3  0.27  0.25
 0.241    8226  98.38    97.6    92.5  0.20  0.18     434    93.2    89.8  0.25  0.23
 0.310    9284  97.93    60.3    57.2  0.19  0.17     489    61.7    58.3  0.24  0.22
 0.378   10168  97.35    41.7    39.1  0.21  0.19     533    42.7    40.2  0.27  0.25
 0.447   10969  96.45    32.2    29.2  0.25  0.24     576    32.3    29.1  0.29  0.28
 0.516   11666  96.05    25.1    22.6  0.29  0.29     626    25.8    23.0  0.31  0.31
 0.584   12407  95.38    20.3    18.1  0.35  0.35     650    20.0    18.0  0.36  0.37
 0.653   12971  94.82    17.2    15.0  0.38  0.38     699    17.4    14.9  0.37  0.37
 0.722   13492  94.03    14.7    12.8  0.42  0.43     754    14.7    12.6  0.42  0.44
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0349   2851   0.889    218   0.792   3069   0.882  0.942  0.9449  0.9532  0.8803  0.8597
  0.1036   5232   0.844    229   0.743   5461   0.840  1.003  0.9164  0.9335  0.8429  0.8881
  0.1723   6783   0.809    215   0.714   6998   0.806  0.969  0.9177  0.9273  0.8168  0.8797
  0.2410   7998   0.815    228   0.690   8226   0.812  0.999  0.9156  0.9365  0.8356  0.9001
  0.3097   9059   0.776    225   0.710   9284   0.775  0.975  0.9172  0.9340  0.8516  0.9114
  0.3783   9941   0.682    227   0.626  10168   0.680  0.929  0.8879  0.9087  0.7932  0.8824
  0.4470  10735   0.590    234   0.565  10969   0.590  0.898  0.8585  0.8770  0.7573  0.8378
  0.5157  11438   0.510    228   0.490  11666   0.509  0.796  0.8151  0.8245  0.6934  0.7311
  0.5844  12169   0.385    238   0.356  12407   0.384  0.680  0.7313  0.7499  0.5037  0.6095
  0.6531  12750   0.317    221   0.331  12971   0.317  0.614  0.6795  0.7005  0.5035  0.4813
  0.7218  13295   0.336    224   0.326  13519   0.336  0.593  0.6717  0.6888  0.3531  0.2885
 $$
Resolution limits                    =     42.684     1.150
Number of used reflections           =     104738
Percentage observed                  =    96.4985
Percentage of free reflections       =     5.0581
Overall R factor                     =     0.2337
Free R factor                        =     0.2712
Average Fourier shell correlation    =     0.8313
AverageFree Fourier shell correlation=     0.8129
Overall weighted R factor            =     0.2217
Free weighted R factor               =     0.2569
Overall weighted R2 factor           =     0.2926
Free weighted R2 factor              =     0.2807
Average correlation coefficient      =     0.7057
Overall correlation coefficient      =     0.9524
Free correlation coefficient         =     0.9416
Cruickshanks DPI for coordinate error=     0.0477
DPI based on free R factor           =     0.0492
Overall figure of merit              =     0.5686
ML based su of positional parameters =     0.0748
ML based su of thermal parameters    =     4.1846
-----------------------------------------------------------------------------
  Time in seconds: CPU =        93.57
             Elapsed =         128.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2306   0.2714   0.610      441712.   24009.4   0.0140  1.048   1.793  1.108   0.090
       1   0.2311   0.2710   0.585      452289.   24557.1   0.0150  1.120   1.858  1.149   0.094
       2   0.2313   0.2709   0.578      455063.   24706.5   0.0152  1.131   1.867  1.155   0.095
       3   0.2318   0.2710   0.576      457091.   24814.6   0.0152  1.137   1.874  1.159   0.095
       4   0.2324   0.2710   0.572      459876.   24957.7   0.0152  1.131   1.875  1.158   0.095
       5   0.2331   0.2710   0.573      461434.   25029.4   0.0150  1.117   1.868  1.154   0.094
       6   0.2332   0.2710   0.573      461533.   25028.5   0.0150  1.115   1.868  1.154   0.094
       7   0.2335   0.2712   0.570      463036.   25111.8   0.0149  1.113   1.869  1.154   0.094
       8   0.2336   0.2711   0.569      463426.   25132.8   0.0149  1.112   1.869  1.154   0.094
       9   0.2336   0.2712   0.569      463417.   25132.3   0.0149  1.112   1.869  1.154   0.094
      10   0.2337   0.2712   0.569      463561.   25139.5   0.0149  1.112   1.869  1.154   0.094
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2306   0.2337
             R free    0.2714   0.2712
     Rms BondLength    0.0140   0.0149
      Rms BondAngle    1.7933   1.8690
     Rms ChirVolume    0.0902   0.0944
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:     129.8s System:    0.6s Elapsed:     2:10