###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 11:54:11 


 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 1.20     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_1-25A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - EP_R00_1-20A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - EP_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - EP_R00_1-20A.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       0.0631
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    42.6836  1.2000
  Estimated number of reflections :     142788
  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  1.2000

  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_1-25A.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       5046
Number of   all  reflections     100646
--------------------------------------------------------------------------------
 Number of reflections in file     149916
 Number of reflections read         100646

   Current auto weighting coefficient =    5.4997053    

 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.= 0.915 id.= 2.950 dev= -2.04 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        :   126  198  144
 Maximuum H,K,L                 :    38   61   44
 Minimum acceptable grid spacing:    82  132   95
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   126  198  144
 Maximuum H,K,L                 :    38   61   44
 Minimum acceptable grid spacing:    82  132   95
 Weight matrix   0.27379021    
 Actual weight    5.4997053      is applied to the X-ray term
Norm of X_ray positional gradient                62.9
Norm of Geom. positional gradient                97.1
Norm of X_ray B-factor gradient                  80.5
Norm of Geom. B-factor gradient                 0.162E+04
Product of X_ray and Geom posit. gradients     -0.410E+08
 Cosine of angle between them                      -0.481
Product of X_ray and Geom B-fact gradients     -0.144E+08
 Cosine of angle between them                      -0.007


Residuals: XRAY=     0.2101E+07 GEOM=     0.2229E+05 TOTAL=     0.2124E+07
 function value    2123720.5    

-------------------------------------------------------------------------------
             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     1.766     1.637
Bond angles  : others                          5115     2.541     1.563
Torsion angles, period  1. refined              363     6.928     5.000
Torsion angles, period  2. refined               86    29.619    25.000
Torsion angles, period  3. refined              342    10.416    15.000
Torsion angles, period  4. refined                1    15.041    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.013     0.020
Planar groups: others                           524     0.023     0.020
VDW repulsions: refined_atoms                   430     0.241     0.200
VDW repulsions.others                          1915     0.227     0.200
VDW; torsion: refined_atoms                    1288     0.173     0.200
VDW; torsion.others                            1066     0.080     0.200
HBOND: refined_atoms                             39     0.121     0.200
VDW repulsions: symmetry: refined_atoms           2     0.076     0.200
VDW repulsions: symmetry: others                 25     0.147     0.200
HBOND: symmetry: refined_atoms                    3     0.031     0.200
M. chain bond B values: refined atoms          1369     1.880     1.343
M. chain bond B values: others                 1368     1.883  8089.801
M. chain angle B values: refined atoms         1719     2.182     2.034
M. chain angle B values: others                1720     2.181    11.069
S. chain bond B values: refined atoms          1164     2.376     1.462
S. chain bond B values: others                 1164     2.376**********
S. chain angle B values: refined atoms         1765     2.652     2.140
S. chain angle B values: others                1765     2.651     2.140
Long range B values: refined atoms             2680     2.613    16.187
Long range B values: others                    2681     2.613    20.752
Rigid bond restraints                          2533     4.034     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -0.1590
Partial structure    1: scale =     0.5027, B  =   38.3285
Overall anisotropic scale factors
   B11 =   0.46 B22 =   0.04 B33 =   0.10 B12 =   0.00 B13 =  -0.90 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    2720  99.55   285.6   297.6  0.21  0.23     144   271.0   288.2  0.22  0.23
 0.095    4800  99.37   225.6   207.2  0.21  0.21     255   220.7   209.3  0.26  0.26
 0.158    6173  98.96   133.9   131.8  0.21  0.20     323   133.6   134.6  0.26  0.25
 0.221    7266  98.43   107.1   101.0  0.20  0.18     382   104.0    99.3  0.25  0.23
 0.284    8171  98.17    71.8    68.1  0.18  0.16     431    71.6    68.1  0.24  0.22
 0.347    8967  97.57    47.9    45.0  0.18  0.16     468    47.8    46.1  0.26  0.24
 0.411    9672  96.93    36.6    34.1  0.21  0.19     510    37.7    34.6  0.27  0.26
 0.474   10336  96.35    29.2    26.7  0.25  0.24     558    29.6    27.1  0.30  0.29
 0.537   10953  95.82    23.1    21.4  0.32  0.32     565    23.2    21.5  0.33  0.33
 0.600   11486  95.33    19.5    17.8  0.37  0.37     623    19.4    18.2  0.37  0.38
 0.663   11983  94.57    16.9    15.4  0.40  0.40     640    17.0    15.0  0.38  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   2514   0.881    206   0.765   2720   0.872  0.926  0.9427  0.9529  0.8862  0.8709
  0.0952   4593   0.847    207   0.742   4800   0.843  1.009  0.9217  0.9334  0.8552  0.8904
  0.1583   5977   0.822    196   0.715   6173   0.818  0.959  0.9150  0.9271  0.8253  0.8855
  0.2213   7054   0.834    212   0.680   7266   0.830  1.001  0.9142  0.9325  0.8292  0.8979
  0.2844   7968   0.828    203   0.728   8171   0.825  0.982  0.9144  0.9368  0.8390  0.9253
  0.3475   8758   0.798    209   0.694   8967   0.795  0.949  0.8925  0.9177  0.7982  0.9150
  0.4106   9467   0.742    205   0.685   9672   0.741  0.915  0.8669  0.8842  0.7918  0.8857
  0.4737  10119   0.684    217   0.564  10336   0.681  0.857  0.8196  0.8366  0.7338  0.8291
  0.5367  10738   0.615    215   0.552  10953   0.614  0.732  0.7452  0.7595  0.6221  0.6889
  0.5998  11275   0.461    211   0.364  11486   0.459  0.595  0.6247  0.6289  0.4843  0.5654
  0.6629  11815   0.423    200   0.368  12015   0.422  0.544  0.5882  0.5762  0.5024  0.4421
 $$
Resolution limits                    =     42.684     1.200
Number of used reflections           =      92559
Percentage observed                  =    96.8325
Percentage of free reflections       =     5.0278
Overall R factor                     =     0.2231
Free R factor                        =     0.2664
Average Fourier shell correlation    =     0.8116
AverageFree Fourier shell correlation=     0.7988
Overall weighted R factor            =     0.2123
Free weighted R factor               =     0.2519
Overall weighted R2 factor           =     0.2837
Free weighted R2 factor              =     0.2770
Average correlation coefficient      =     0.7660
Overall correlation coefficient      =     0.9532
Free correlation coefficient         =     0.9404
Cruickshanks DPI for coordinate error=     0.0514
DPI based on free R factor           =     0.0536
Overall figure of merit              =     0.6768
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     3.4042
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    382098.41       22291.682       2123720.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25102749    
 Actual weight    5.4997053      is applied to the X-ray term


 function value    2145838.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.019     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -0.3611
Partial structure    1: scale =     0.5046, B  =   38.4632
Overall anisotropic scale factors
   B11 =   0.67 B22 =   0.03 B33 =   0.00 B12 =   0.00 B13 =  -1.01 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2230
Free R factor                        =     0.2661
Average Fourier shell correlation    =     0.8122
AverageFree Fourier shell correlation=     0.7978
Average correlation coefficient      =     0.7697
Overall figure of merit              =     0.6533
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02


 fvalues    388585.94       14797.590       2183704.3       2123720.5    

 fvalues    388585.94       14797.590       2167917.5       2151905.8    
 fvalues    388585.94       14797.590       2167917.5       2151905.8    


     CGMAT cycle number =      3

 Weight matrix   0.22287020    
 Actual weight    4.9997320      is applied to the X-ray term


 function value    1960392.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.017     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -0.4008
Partial structure    1: scale =     0.5055, B  =   38.5008
Overall anisotropic scale factors
   B11 =   0.74 B22 =   0.02 B33 =  -0.03 B12 =   0.00 B13 =  -1.03 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2230
Free R factor                        =     0.2660
Average Fourier shell correlation    =     0.8127
AverageFree Fourier shell correlation=     0.7980
Average correlation coefficient      =     0.7697
Overall figure of merit              =     0.6469
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    389245.16       14271.265       1960392.8       2151905.8    


     CGMAT cycle number =      4

 Weight matrix   0.19384049    
 Actual weight    4.5452108      is applied to the X-ray term


 function value    1796917.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.013     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0482, B  =   -0.4664
Partial structure    1: scale =     0.5055, B  =   38.4942
Overall anisotropic scale factors
   B11 =   0.85 B22 =   0.01 B33 =  -0.08 B12 =   0.00 B13 =  -1.08 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2232
Free R factor                        =     0.2661
Average Fourier shell correlation    =     0.8113
AverageFree Fourier shell correlation=     0.7957
Average correlation coefficient      =     0.7698
Overall figure of merit              =     0.6344
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    392347.28       13616.650       1796917.8       1960392.8    


     CGMAT cycle number =      5

 Weight matrix   0.17152238    
 Actual weight    4.1320100      is applied to the X-ray term


 function value    1646056.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.011     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.5275
Partial structure    1: scale =     0.5055, B  =   38.5325
Overall anisotropic scale factors
   B11 =   0.96 B22 =  -0.00 B33 =  -0.14 B12 =   0.00 B13 =  -1.12 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2234
Free R factor                        =     0.2660
Average Fourier shell correlation    =     0.8152
AverageFree Fourier shell correlation=     0.7990
Average correlation coefficient      =     0.7697
Overall figure of merit              =     0.6279
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    395163.81       13235.755       1646056.6       1796917.8    


     CGMAT cycle number =      6

 Weight matrix   0.16815567    
 Actual weight    4.1320100      is applied to the X-ray term


 function value    1656532.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.5950
Partial structure    1: scale =     0.5057, B  =   38.5636
Overall anisotropic scale factors
   B11 =   1.08 B22 =  -0.02 B33 =  -0.20 B12 =   0.00 B13 =  -1.16 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2238
Free R factor                        =     0.2657
Average Fourier shell correlation    =     0.8208
AverageFree Fourier shell correlation=     0.8045
Average correlation coefficient      =     0.7694
Overall figure of merit              =     0.6237
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    397610.06       13068.254       1666787.1       1646056.6    

 fvalues    397610.06       13068.254       1661252.3       1655997.0    
 fvalues    397610.06       13068.254       1661252.3       1655997.0    


     CGMAT cycle number =      7

 Weight matrix   0.16739422    
 Actual weight    4.1320100      is applied to the X-ray term


 function value    1658558.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.6112
Partial structure    1: scale =     0.5059, B  =   38.5901
Overall anisotropic scale factors
   B11 =   1.11 B22 =  -0.02 B33 =  -0.22 B12 =   0.00 B13 =  -1.17 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2239
Free R factor                        =     0.2657
Average Fourier shell correlation    =     0.8224
AverageFree Fourier shell correlation=     0.8061
Average correlation coefficient      =     0.7694
Overall figure of merit              =     0.6232
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    398232.81       13064.467       1663252.1       1655997.0    

 fvalues    398232.81       13064.467       1660940.3       1658566.5    
 fvalues    398232.81       13064.467       1660940.3       1658566.5    


     CGMAT cycle number =      8

 Weight matrix   0.16690807    
 Actual weight    4.1320100      is applied to the X-ray term


 function value    1659715.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.6180
Partial structure    1: scale =     0.5060, B  =   38.5872
Overall anisotropic scale factors
   B11 =   1.12 B22 =  -0.02 B33 =  -0.22 B12 =   0.00 B13 =  -1.17 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2240
Free R factor                        =     0.2657
Average Fourier shell correlation    =     0.8228
AverageFree Fourier shell correlation=     0.8065
Average correlation coefficient      =     0.7693
Overall figure of merit              =     0.6225
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    398517.41       13066.243       1661603.4       1658566.5    

 fvalues    398517.41       13066.243       1660739.8       1659744.1    
 fvalues    398517.41       13066.243       1660739.8       1659744.1    


     CGMAT cycle number =      9

 Weight matrix   0.16671515    
 Actual weight    4.1320100      is applied to the X-ray term


 function value    1660279.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.6243
Partial structure    1: scale =     0.5059, B  =   38.5818
Overall anisotropic scale factors
   B11 =   1.12 B22 =  -0.02 B33 =  -0.22 B12 =   0.00 B13 =  -1.17 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2240
Free R factor                        =     0.2656
Average Fourier shell correlation    =     0.8230
AverageFree Fourier shell correlation=     0.8066
Average correlation coefficient      =     0.7693
Overall figure of merit              =     0.6223
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    398647.63       13063.978       1660841.8       1659744.1    

 fvalues    398647.63       13063.978       1660472.6       1660280.0    
 fvalues    398647.63       13063.978       1660472.6       1660280.0    


     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.= 0.983 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        :   126  198  144
 Maximuum H,K,L                 :    38   61   44
 Minimum acceptable grid spacing:    82  132   95
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   126  198  144
 Maximuum H,K,L                 :    38   61   44
 Minimum acceptable grid spacing:    82  132   95
 Weight matrix   0.16666248    
 Actual weight    4.1320100      is applied to the X-ray term
Norm of X_ray positional gradient                53.8
Norm of Geom. positional gradient                55.6
Norm of X_ray B-factor gradient                  77.1
Norm of Geom. B-factor gradient                  316.
Product of X_ray and Geom posit. gradients     -0.381E+08
 Cosine of angle between them                      -0.913
Product of X_ray and Geom B-fact gradients     -0.146E+08
 Cosine of angle between them                      -0.035


Residuals: XRAY=     0.1647E+07 GEOM=     0.1306E+05 TOTAL=     0.1660E+07
 function value    1660344.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.008     0.017
Bond angles  : refined atoms                   3498     1.794     1.637
Bond angles  : others                          5115     1.622     1.563
Torsion angles, period  1. refined              363     6.970     5.000
Torsion angles, period  2. refined               86    29.771    25.000
Torsion angles, period  3. refined              342    10.456    15.000
Torsion angles, period  4. refined                1    14.931    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.012     0.020
Planar groups: others                           524     0.005     0.020
VDW repulsions: refined_atoms                   432     0.240     0.200
VDW repulsions.others                          1912     0.205     0.200
VDW; torsion: refined_atoms                    1289     0.173     0.200
VDW; torsion.others                            1097     0.083     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     0.143     0.200
HBOND: symmetry: refined_atoms                    3     0.022     0.200
M. chain bond B values: refined atoms          1369     1.773     1.318
M. chain bond B values: others                 1368     1.775  8293.981
M. chain angle B values: refined atoms         1719     2.069     1.996
M. chain angle B values: others                1720     2.068    11.004
S. chain bond B values: refined atoms          1164     2.232     1.438
S. chain bond B values: others                 1164     2.232**********
S. chain angle B values: refined atoms         1765     2.505     2.103
S. chain angle B values: others                1765     2.504     2.103
Long range B values: refined atoms             2679     2.496    15.900
Long range B values: others                    2680     2.496    15.900
Rigid bond restraints                          2533     7.608     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.6222
Partial structure    1: scale =     0.5060, B  =   38.5917
Overall anisotropic scale factors
   B11 =   1.12 B22 =  -0.02 B33 =  -0.22 B12 =   0.00 B13 =  -1.17 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    2720  99.55   286.4   298.0  0.21  0.23     144   271.7   288.5  0.22  0.22
 0.095    4800  99.37   226.2   207.5  0.22  0.21     255   221.3   209.4  0.26  0.26
 0.158    6173  98.96   134.3   132.1  0.21  0.20     323   134.0   134.8  0.26  0.24
 0.221    7266  98.43   107.4   101.3  0.20  0.18     382   104.3    99.8  0.25  0.23
 0.284    8171  98.17    72.0    68.5  0.18  0.16     431    71.8    68.4  0.24  0.22
 0.347    8967  97.57    48.0    45.2  0.19  0.17     468    48.0    46.2  0.26  0.24
 0.411    9672  96.93    36.7    34.1  0.21  0.20     510    37.8    34.7  0.27  0.26
 0.474   10336  96.35    29.3    26.7  0.25  0.25     558    29.7    27.0  0.30  0.29
 0.537   10953  95.82    23.2    21.4  0.31  0.32     565    23.2    21.5  0.33  0.33
 0.600   11486  95.33    19.5    17.8  0.37  0.37     623    19.4    18.1  0.37  0.37
 0.663   11983  94.57    16.9    15.3  0.39  0.39     640    17.0    14.9  0.38  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   2514   0.898    206   0.789   2720   0.889  0.929  0.9477  0.9578  0.8853  0.8688
  0.0952   4593   0.848    207   0.748   4800   0.844  1.009  0.9227  0.9347  0.8549  0.8892
  0.1583   5977   0.824    196   0.729   6173   0.821  0.959  0.9194  0.9296  0.8285  0.8845
  0.2213   7054   0.828    212   0.682   7266   0.824  1.001  0.9158  0.9342  0.8311  0.8972
  0.2844   7968   0.816    203   0.724   8171   0.813  0.982  0.9168  0.9394  0.8385  0.9226
  0.3475   8758   0.774    209   0.685   8967   0.772  0.949  0.8967  0.9214  0.8033  0.9109
  0.4106   9467   0.672    205   0.646   9672   0.672  0.911  0.8629  0.8818  0.7919  0.8802
  0.4737  10119   0.604    217   0.529  10336   0.603  0.850  0.8251  0.8429  0.7303  0.8235
  0.5367  10738   0.508    215   0.477  10953   0.508  0.705  0.7406  0.7640  0.6286  0.6972
  0.5998  11275   0.400    211   0.350  11486   0.399  0.612  0.6722  0.6831  0.4912  0.5789
  0.6629  11815   0.302    200   0.293  12015   0.301  0.520  0.5953  0.5964  0.4992  0.4637
 $$
Resolution limits                    =     42.684     1.200
Number of used reflections           =      92559
Percentage observed                  =    96.8325
Percentage of free reflections       =     5.0278
Overall R factor                     =     0.2240
Free R factor                        =     0.2656
Average Fourier shell correlation    =     0.8230
AverageFree Fourier shell correlation=     0.8067
Overall weighted R factor            =     0.2131
Free weighted R factor               =     0.2513
Overall weighted R2 factor           =     0.2869
Free weighted R2 factor              =     0.2768
Average correlation coefficient      =     0.7693
Overall correlation coefficient      =     0.9526
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.0516
DPI based on free R factor           =     0.0534
Overall figure of merit              =     0.6222
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     3.8867
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    398665.66       13063.410       1660781.3       1660280.0    

 fvalues    398665.66       13063.410       1660507.5       1660353.9    
 fvalues    398665.66       13063.410       1660507.5       1660353.9    

    ****                              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.= 0.983 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_1-20A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.008     0.017
Bond angles  : refined atoms                   3498     1.794     1.637
Bond angles  : others                          5115     1.622     1.563
Torsion angles, period  1. refined              363     6.970     5.000
Torsion angles, period  2. refined               86    29.771    25.000
Torsion angles, period  3. refined              342    10.456    15.000
Torsion angles, period  4. refined                1    14.932    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.012     0.020
Planar groups: others                           524     0.005     0.020
VDW repulsions: refined_atoms                   432     0.240     0.200
VDW repulsions.others                          1912     0.205     0.200
VDW; torsion: refined_atoms                    1289     0.173     0.200
VDW; torsion.others                            1097     0.083     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     0.143     0.200
HBOND: symmetry: refined_atoms                    3     0.022     0.200
M. chain bond B values: refined atoms          1369     1.773     1.317
M. chain bond B values: others                 1368     1.775  8294.246
M. chain angle B values: refined atoms         1719     2.069     1.996
M. chain angle B values: others                1720     2.068    11.005
S. chain bond B values: refined atoms          1164     2.232     1.438
S. chain bond B values: others                 1164     2.231**********
S. chain angle B values: refined atoms         1765     2.504     2.103
S. chain angle B values: others                1765     2.504     2.103
Long range B values: refined atoms             2679     2.496    15.900
Long range B values: others                    2680     2.496    15.900
Rigid bond restraints                          2533     7.614     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0481, B  =   -0.6229
Partial structure    1: scale =     0.5060, B  =   38.5918
Overall anisotropic scale factors
   B11 =   1.13 B22 =  -0.02 B33 =  -0.23 B12 =   0.00 B13 =  -1.17 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.032    2720  99.55   286.4   298.0  0.21  0.23     144   271.7   288.5  0.22  0.22
 0.095    4800  99.37   226.2   207.5  0.22  0.21     255   221.3   209.4  0.26  0.26
 0.158    6173  98.96   134.3   132.1  0.21  0.20     323   134.0   134.8  0.26  0.24
 0.221    7266  98.43   107.4   101.4  0.20  0.18     382   104.3    99.8  0.25  0.23
 0.284    8171  98.17    72.0    68.5  0.18  0.16     431    71.8    68.4  0.24  0.22
 0.347    8967  97.57    48.0    45.2  0.19  0.17     468    48.0    46.2  0.26  0.24
 0.411    9672  96.93    36.7    34.1  0.21  0.20     510    37.8    34.7  0.27  0.26
 0.474   10336  96.35    29.3    26.7  0.25  0.25     558    29.7    27.0  0.30  0.29
 0.537   10953  95.82    23.2    21.4  0.31  0.32     565    23.2    21.5  0.33  0.33
 0.600   11486  95.33    19.5    17.8  0.37  0.37     623    19.4    18.1  0.37  0.37
 0.663   11983  94.57    16.9    15.3  0.39  0.39     640    17.0    14.9  0.38  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0321   2514   0.898    206   0.789   2720   0.889  0.929  0.9477  0.9578  0.8853  0.8688
  0.0952   4593   0.848    207   0.748   4800   0.844  1.009  0.9227  0.9347  0.8549  0.8892
  0.1583   5977   0.824    196   0.729   6173   0.821  0.959  0.9194  0.9296  0.8285  0.8845
  0.2213   7054   0.828    212   0.682   7266   0.824  1.001  0.9158  0.9342  0.8311  0.8972
  0.2844   7968   0.815    203   0.724   8171   0.813  0.982  0.9168  0.9393  0.8385  0.9226
  0.3475   8758   0.774    209   0.685   8967   0.772  0.949  0.8967  0.9214  0.8033  0.9109
  0.4106   9467   0.672    205   0.646   9672   0.672  0.911  0.8629  0.8819  0.7919  0.8802
  0.4737  10119   0.604    217   0.529  10336   0.603  0.850  0.8251  0.8429  0.7303  0.8235
  0.5367  10738   0.508    215   0.477  10953   0.507  0.705  0.7406  0.7640  0.6286  0.6972
  0.5998  11275   0.400    211   0.350  11486   0.399  0.612  0.6722  0.6832  0.4912  0.5789
  0.6629  11815   0.301    200   0.293  12015   0.301  0.520  0.5954  0.5965  0.4991  0.4637
 $$
Resolution limits                    =     42.684     1.200
Number of used reflections           =      92559
Percentage observed                  =    96.8325
Percentage of free reflections       =     5.0278
Overall R factor                     =     0.2240
Free R factor                        =     0.2656
Average Fourier shell correlation    =     0.8230
AverageFree Fourier shell correlation=     0.8067
Overall weighted R factor            =     0.2131
Free weighted R factor               =     0.2514
Overall weighted R2 factor           =     0.2870
Free weighted R2 factor              =     0.2768
Average correlation coefficient      =     0.7693
Overall correlation coefficient      =     0.9526
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.0516
DPI based on free R factor           =     0.0534
Overall figure of merit              =     0.6221
ML based su of positional parameters =     0.0690
ML based su of thermal parameters    =     3.8867
-----------------------------------------------------------------------------
  Time in seconds: CPU =        97.67
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2231   0.2664   0.677      382098.   20730.9   0.0137  1.028   1.766  1.089   0.090
       1   0.2230   0.2661   0.653      387483.   21020.9   0.0142  1.066   1.799  1.111   0.092
       2   0.2230   0.2660   0.647      389245.   21111.9   0.0143  1.074   1.805  1.115   0.093
       3   0.2232   0.2661   0.634      392347.   21279.4   0.0143  1.076   1.808  1.117   0.092
       4   0.2234   0.2660   0.628      395164.   21428.0   0.0142  1.067   1.804  1.114   0.092
       5   0.2238   0.2657   0.624      397740.   21560.7   0.0140  1.052   1.796  1.109   0.090
       6   0.2239   0.2657   0.623      398231.   21585.5   0.0140  1.049   1.794  1.108   0.090
       7   0.2240   0.2657   0.622      398511.   21599.7   0.0140  1.048   1.794  1.108   0.090
       8   0.2240   0.2656   0.622      398648.   21606.7   0.0140  1.048   1.794  1.108   0.090
       9   0.2240   0.2656   0.622      398663.   21607.6   0.0140  1.048   1.794  1.108   0.090
      10   0.2240   0.2656   0.622      398685.   21608.7   0.0140  1.048   1.794  1.108   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2231   0.2240
             R free    0.2664   0.2656
     Rms BondLength    0.0137   0.0140
      Rms BondAngle    1.7661   1.7940
     Rms ChirVolume    0.0903   0.0902
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:     133.7s System:    0.5s Elapsed:     2:15