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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: malyma  Run date: 12/ 3/2021 Run time: 11:04:46 


 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 47.32 2.00     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- weight matrix 0.0600
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli_webinar_R00_2-10A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_webinar_R00_2-00A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_webinar_R00_2-00A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  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:     5       0.0500
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.0000
  Estimated number of reflections :      40320
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0600
  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:    47.3245  2.0000

  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 :poli_webinar_R00_2-10A.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    :    2286
  Number of residues :     307
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  BBB  is missing in the structure
  ATTENTION: atom:OXT  THR                70  BBB  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  BBB  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  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:      4485         0      4485
               Angles:      8175         0      8175
              Chirals:       284         0       284
               Planes:       646         0       646
             Torsions:      2321         0      2321
            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       1483
Number of   all  reflections      30492
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          30492

   Current auto weighting coefficient =    7.4995480    

 mode : HKRF


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



     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Weight matrix   5.99999987E-02
 Actual weight    21.440447      is applied to the X-ray term
Norm of X_ray positional gradient                34.0
Norm of Geom. positional gradient                77.4
Norm of X_ray B-factor gradient                  36.0
Norm of Geom. B-factor gradient                  30.9
Product of X_ray and Geom posit. gradients     -0.128E+08
 Cosine of angle between them                      -0.362
Product of X_ray and Geom B-fact gradients     -0.381E+07
 Cosine of angle between them                      -0.763


Residuals: XRAY=     0.2546E+07 GEOM=     0.1832E+05 TOTAL=     0.2564E+07
 function value    2563893.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.957     1.648
Bond angles  : others                          5121     2.282     1.582
Torsion angles, period  1. refined              265     7.613     5.000
Torsion angles, period  2. refined              135    32.876    22.370
Torsion angles, period  3. refined              475    20.558    15.000
Torsion angles, period  4. refined               19    20.607    15.000
Chiral centres: refined atoms                   284     0.087     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.014     0.020
VDW repulsions: refined_atoms                   539     0.232     0.200
VDW repulsions.others                          1981     0.225     0.200
VDW; torsion: refined_atoms                    1098     0.174     0.200
VDW; torsion.others                            1052     0.082     0.200
HBOND: refined_atoms                             55     0.197     0.200
HBOND.others                                      1     0.023     0.200
VDW repulsions: symmetry: refined_atoms          11     0.214     0.200
VDW repulsions: symmetry: others                 33     0.239     0.200
HBOND: symmetry: refined_atoms                    2     0.149     0.200
M. chain bond B values: refined atoms          1075     7.863     6.990
M. chain bond B values: others                 1074     7.818     6.980
M. chain angle B values: refined atoms         1335    10.001    10.430
M. chain angle B values: others                1336    10.002    10.439
S. chain bond B values: refined atoms          1209     9.181     7.791
S. chain bond B values: others                 1207     9.182     7.783
S. chain angle B values: refined atoms         1719    12.703    11.348
S. chain angle B values: others                1719    12.699    11.348
Long range B values: refined atoms             2619    14.607    80.055
Long range B values: others                    2619    14.622    80.096
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5167, B  =   -1.1861
Partial structure    1: scale =     0.3857, B  =   55.4990
Overall anisotropic scale factors
   B11 =   5.08 B22 =  -1.59 B33 =  -3.49 B12 =   0.00 B13 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   271.9   270.4  0.20  0.21     125   261.2   260.6  0.30  0.31
 0.075    4806  99.90   155.8   144.0  0.20  0.19     260   157.9   146.0  0.27  0.25
 0.125    6062  99.74    54.4    53.5  0.25  0.21     344    54.2    54.6  0.34  0.32
 0.175    7199  99.91    28.1    26.5  0.36  0.33     331    28.7    27.6  0.39  0.36
 0.225    8050  99.26    19.9    12.7  0.48  0.49     417    19.7    12.2  0.48  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.813    625   0.746   2782   0.798  0.921  0.9077  0.9430  0.8495  0.9291
  0.0753   4157   0.823    649   0.741   4806   0.812  1.005  0.9129  0.9360  0.8503  0.9328
  0.1252   5428   0.707    634   0.640   6062   0.700  0.874  0.8321  0.8711  0.7296  0.8883
  0.1751   6547   0.495    652   0.450   7199   0.491  0.653  0.6219  0.6383  0.7062  0.7753
  0.2250   7412   0.337    645   0.303   8057   0.334  0.590  0.3556  0.3566  0.5898  0.5590
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2420
Free R factor                        =     0.3169
Average Fourier shell correlation    =     0.6874
AverageFree Fourier shell correlation=     0.6711
Overall weighted R factor            =     0.2142
Free weighted R factor               =     0.2918
Overall weighted R2 factor           =     0.2277
Free weighted R2 factor              =     0.3168
Average correlation coefficient      =     0.7798
Overall correlation coefficient      =     0.9614
Free correlation coefficient         =     0.9194
Cruickshanks DPI for coordinate error=     0.1676
DPI based on free R factor           =     0.1814
Overall figure of merit              =     0.5739
ML based su of positional parameters =     0.2642
ML based su of thermal parameters    =    11.4026
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    118727.68       18318.945       2563893.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   5.99999949E-02
 Actual weight    21.979788      is applied to the X-ray term


 function value    2619297.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5159, B  =   -0.2627
Partial structure    1: scale =     0.3858, B  =   54.8735
Overall anisotropic scale factors
   B11 =   5.03 B22 =  -1.59 B33 =  -3.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2418
Free R factor                        =     0.3156
Average Fourier shell correlation    =     0.6630
AverageFree Fourier shell correlation=     0.6505
Average correlation coefficient      =     0.7841
Overall figure of merit              =     0.5476
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02


 fvalues    118527.12       12075.067       2618315.3       2563893.5    

 fvalues    118527.12       12075.067       2618002.0       2617276.0    
 fvalues    118527.12       12075.067       2618002.0       2617276.0    


     CGMAT cycle number =      3

 Weight matrix   6.00000024E-02
 Actual weight    21.156311      is applied to the X-ray term


 function value    2520851.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5164, B  =   -0.1695
Partial structure    1: scale =     0.3860, B  =   54.7075
Overall anisotropic scale factors
   B11 =   5.01 B22 =  -1.58 B33 =  -3.43 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2416
Free R factor                        =     0.3158
Average Fourier shell correlation    =     0.6735
AverageFree Fourier shell correlation=     0.6618
Average correlation coefficient      =     0.7834
Overall figure of merit              =     0.5587
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    118577.52       12188.383       2520851.5       2617276.0    


     CGMAT cycle number =      4

 Weight matrix   5.99999987E-02
 Actual weight    20.641279      is applied to the X-ray term


 function value    2457634.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5176, B  =   -0.0497
Partial structure    1: scale =     0.3859, B  =   54.6436
Overall anisotropic scale factors
   B11 =   5.01 B22 =  -1.58 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3160
Average Fourier shell correlation    =     0.6778
AverageFree Fourier shell correlation=     0.6657
Average correlation coefficient      =     0.7830
Overall figure of merit              =     0.5657
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    118470.01       12261.525       2457634.0       2520851.5    


     CGMAT cycle number =      5

 Weight matrix   5.99999949E-02
 Actual weight    21.273043      is applied to the X-ray term


 function value    2533673.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5191, B  =    0.0035
Partial structure    1: scale =     0.3856, B  =   54.5193
Overall anisotropic scale factors
   B11 =   5.00 B22 =  -1.58 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3163
Average Fourier shell correlation    =     0.6728
AverageFree Fourier shell correlation=     0.6608
Average correlation coefficient      =     0.7830
Overall figure of merit              =     0.5575
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    118446.05       12257.076       2532973.8       2457634.0    

 fvalues    118446.05       12257.076       2533611.8       2531965.0    
 fvalues    118446.05       12257.076       2533611.8       2531965.0    


     CGMAT cycle number =      6

 Weight matrix   5.99999949E-02
 Actual weight    21.345131      is applied to the X-ray term


 function value    2542085.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5195, B  =    0.0048
Partial structure    1: scale =     0.3856, B  =   54.5081
Overall anisotropic scale factors
   B11 =   5.00 B22 =  -1.58 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3163
Average Fourier shell correlation    =     0.6721
AverageFree Fourier shell correlation=     0.6601
Average correlation coefficient      =     0.7830
Overall figure of merit              =     0.5564
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    118393.20       12272.396       2541448.5       2531965.0    

 fvalues    118393.20       12272.396       2541341.5       2539390.8    
 fvalues    118393.20       12272.396       2541341.5       2539390.8    


     CGMAT cycle number =      7

 Weight matrix   6.00000024E-02
 Actual weight    21.072588      is applied to the X-ray term


 function value    2509245.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5195, B  =   -0.0017
Partial structure    1: scale =     0.3857, B  =   54.5400
Overall anisotropic scale factors
   B11 =   5.00 B22 =  -1.58 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3164
Average Fourier shell correlation    =     0.6746
AverageFree Fourier shell correlation=     0.6624
Average correlation coefficient      =     0.7830
Overall figure of merit              =     0.5602
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02
 fvalues    118493.56       12279.251       2509245.3       2539390.8    


     CGMAT cycle number =      8

 Weight matrix   6.00000061E-02
 Actual weight    20.660624      is applied to the X-ray term


 function value    2459132.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5195, B  =   -0.0001
Partial structure    1: scale =     0.3857, B  =   54.5423
Overall anisotropic scale factors
   B11 =   5.00 B22 =  -1.58 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3164
Average Fourier shell correlation    =     0.6776
AverageFree Fourier shell correlation=     0.6652
Average correlation coefficient      =     0.7829
Overall figure of merit              =     0.5655
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    118430.50       12284.282       2459132.3       2509245.3    


     CGMAT cycle number =      9

 Weight matrix   5.99999987E-02
 Actual weight    21.252483      is applied to the X-ray term


 function value    2530878.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5198, B  =    0.0077
Partial structure    1: scale =     0.3858, B  =   54.5546
Overall anisotropic scale factors
   B11 =   4.99 B22 =  -1.57 B33 =  -3.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2415
Free R factor                        =     0.3164
Average Fourier shell correlation    =     0.6732
AverageFree Fourier shell correlation=     0.6611
Average correlation coefficient      =     0.7830
Overall figure of merit              =     0.5579
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    118430.45       12282.137       2530840.0       2459132.3    

 fvalues    118430.45       12282.137       2530876.0       2529223.5    
 fvalues    118430.45       12282.137       2530876.0       2529223.5    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  160  176
 Maximuum H,K,L                 :    30   40   48
 Minimum acceptable grid spacing:    71   97  115
 Weight matrix   5.99999987E-02
 Actual weight    21.270998      is applied to the X-ray term
Norm of X_ray positional gradient                34.4
Norm of Geom. positional gradient                33.6
Norm of X_ray B-factor gradient                  35.6
Norm of Geom. B-factor gradient                  33.9
Product of X_ray and Geom posit. gradients     -0.155E+08
 Cosine of angle between them                      -0.995
Product of X_ray and Geom B-fact gradients     -0.533E+07
 Cosine of angle between them                      -0.985


Residuals: XRAY=     0.2521E+07 GEOM=     0.1228E+05 TOTAL=     0.2533E+07
 function value    2533057.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.983     1.648
Bond angles  : others                          5121     1.411     1.582
Torsion angles, period  1. refined              265     7.662     5.000
Torsion angles, period  2. refined              135    32.864    22.370
Torsion angles, period  3. refined              475    20.684    15.000
Torsion angles, period  4. refined               19    20.959    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   543     0.234     0.200
VDW repulsions.others                          2009     0.205     0.200
VDW; torsion: refined_atoms                    1099     0.175     0.200
VDW; torsion.others                            1057     0.095     0.200
HBOND: refined_atoms                             59     0.193     0.200
VDW repulsions: symmetry: refined_atoms          11     0.216     0.200
VDW repulsions: symmetry: others                 34     0.230     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.984     6.884
M. chain bond B values: others                 1074     7.967     6.875
M. chain angle B values: refined atoms         1335    10.170    10.268
M. chain angle B values: others                1336    10.171    10.276
S. chain bond B values: refined atoms          1209     9.346     7.714
S. chain bond B values: others                 1207     9.347     7.706
S. chain angle B values: refined atoms         1719    12.958    11.218
S. chain angle B values: others                1719    12.951    11.219
Long range B values: refined atoms             2625    14.896    78.943
Long range B values: others                    2624    14.907    78.969
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5200, B  =    0.0050
Partial structure    1: scale =     0.3857, B  =   54.5292
Overall anisotropic scale factors
   B11 =   4.99 B22 =  -1.57 B33 =  -3.42 B12 =   0.00 B13 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   271.3   270.0  0.20  0.21     125   260.6   260.9  0.30  0.31
 0.075    4806  99.90   155.5   143.9  0.19  0.18     260   157.6   145.8  0.26  0.25
 0.125    6062  99.74    54.3    53.4  0.25  0.22     344    54.1    54.6  0.35  0.32
 0.175    7199  99.91    28.1    26.5  0.36  0.33     331    28.7    27.7  0.38  0.36
 0.225    8050  99.26    19.9    12.7  0.48  0.48     417    19.6    12.2  0.47  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.825    625   0.755   2782   0.810  0.924  0.9107  0.9450  0.8518  0.9284
  0.0753   4157   0.823    649   0.741   4806   0.812  1.005  0.9136  0.9371  0.8519  0.9349
  0.1252   5428   0.729    634   0.660   6062   0.722  0.883  0.8407  0.8789  0.7235  0.8858
  0.1751   6547   0.462    652   0.422   7199   0.458  0.612  0.6064  0.6240  0.7121  0.7801
  0.2250   7412   0.286    645   0.263   8057   0.284  0.504  0.3233  0.3103  0.5934  0.5669
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2415
Free R factor                        =     0.3163
Average Fourier shell correlation    =     0.6730
AverageFree Fourier shell correlation=     0.6609
Overall weighted R factor            =     0.2137
Free weighted R factor               =     0.2919
Overall weighted R2 factor           =     0.2274
Free weighted R2 factor              =     0.3167
Average correlation coefficient      =     0.7829
Overall correlation coefficient      =     0.9615
Free correlation coefficient         =     0.9202
Cruickshanks DPI for coordinate error=     0.1672
DPI based on free R factor           =     0.1811
Overall figure of merit              =     0.5575
ML based su of positional parameters =     0.2629
ML based su of thermal parameters    =    11.4486
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    118429.29       12284.235       2532977.5       2529223.5    

 fvalues    118429.29       12284.235       2532990.8       2531393.5    
 fvalues    118429.29       12284.235       2532990.8       2531393.5    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset 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: poli_webinar_R00_2-00A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.984     1.648
Bond angles  : others                          5121     1.411     1.582
Torsion angles, period  1. refined              265     7.662     5.000
Torsion angles, period  2. refined              135    32.864    22.370
Torsion angles, period  3. refined              475    20.685    15.000
Torsion angles, period  4. refined               19    20.961    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   543     0.234     0.200
VDW repulsions.others                          2009     0.205     0.200
VDW; torsion: refined_atoms                    1099     0.175     0.200
VDW; torsion.others                            1057     0.095     0.200
HBOND: refined_atoms                             59     0.193     0.200
VDW repulsions: symmetry: refined_atoms          11     0.216     0.200
VDW repulsions: symmetry: others                 34     0.230     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.984     6.884
M. chain bond B values: others                 1074     7.967     6.875
M. chain angle B values: refined atoms         1335    10.170    10.268
M. chain angle B values: others                1336    10.172    10.276
S. chain bond B values: refined atoms          1209     9.347     7.714
S. chain bond B values: others                 1207     9.348     7.706
S. chain angle B values: refined atoms         1719    12.959    11.219
S. chain angle B values: others                1719    12.951    11.219
Long range B values: refined atoms             2625    14.896    78.944
Long range B values: others                    2624    14.907    78.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5200, B  =    0.0011
Partial structure    1: scale =     0.3857, B  =   54.5183
Overall anisotropic scale factors
   B11 =   4.99 B22 =  -1.57 B33 =  -3.42 B12 =   0.00 B13 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.025    2782  99.45   271.3   270.0  0.20  0.21     125   260.6   260.9  0.30  0.31
 0.075    4806  99.90   155.5   143.9  0.19  0.18     260   157.6   145.8  0.26  0.25
 0.125    6062  99.74    54.3    53.4  0.25  0.22     344    54.1    54.6  0.35  0.32
 0.175    7199  99.91    28.1    26.5  0.36  0.33     331    28.7    27.7  0.38  0.36
 0.225    8050  99.26    19.9    12.7  0.48  0.48     417    19.6    12.2  0.47  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0254   2157   0.825    625   0.755   2782   0.810  0.924  0.9108  0.9450  0.8520  0.9284
  0.0753   4157   0.823    649   0.741   4806   0.812  1.005  0.9136  0.9371  0.8518  0.9349
  0.1252   5428   0.729    634   0.660   6062   0.722  0.883  0.8407  0.8789  0.7236  0.8858
  0.1751   6547   0.460    652   0.420   7199   0.456  0.608  0.6053  0.6230  0.7121  0.7801
  0.2250   7412   0.284    645   0.262   8057   0.282  0.501  0.3219  0.3088  0.5934  0.5669
 $$
Resolution limits                    =     47.324     2.000
Number of used reflections           =      28906
Percentage observed                  =    99.6360
Percentage of free reflections       =     4.8613
Overall R factor                     =     0.2415
Free R factor                        =     0.3163
Average Fourier shell correlation    =     0.6723
AverageFree Fourier shell correlation=     0.6602
Overall weighted R factor            =     0.2137
Free weighted R factor               =     0.2918
Overall weighted R2 factor           =     0.2274
Free weighted R2 factor              =     0.3167
Average correlation coefficient      =     0.7829
Overall correlation coefficient      =     0.9615
Free correlation coefficient         =     0.9203
Cruickshanks DPI for coordinate error=     0.1672
DPI based on free R factor           =     0.1811
Overall figure of merit              =     0.5566
ML based su of positional parameters =     0.2629
ML based su of thermal parameters    =    11.4486
-----------------------------------------------------------------------------
  Time in seconds: CPU =        35.28
             Elapsed =           0.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2420   0.3169   0.574      118728.    6210.6   0.0127  0.881   1.957  1.161   0.087
       1   0.2418   0.3156   0.548      118619.    6211.4   0.0129  0.900   1.955  1.160   0.087
       2   0.2416   0.3158   0.559      118578.    6209.8   0.0130  0.907   1.966  1.167   0.088
       3   0.2415   0.3160   0.566      118470.    6206.1   0.0131  0.910   1.976  1.173   0.088
       4   0.2415   0.3163   0.557      118526.    6208.7   0.0131  0.906   1.979  1.175   0.088
       5   0.2415   0.3163   0.556      118519.    6208.6   0.0131  0.907   1.981  1.176   0.088
       6   0.2415   0.3164   0.560      118494.    6207.5   0.0131  0.907   1.982  1.176   0.088
       7   0.2415   0.3164   0.566      118431.    6205.1   0.0131  0.908   1.983  1.177   0.088
       8   0.2415   0.3164   0.558      118508.    6208.1   0.0131  0.907   1.983  1.177   0.088
       9   0.2415   0.3163   0.558      118508.    6208.0   0.0131  0.907   1.983  1.177   0.088
      10   0.2415   0.3163   0.557      118507.    6208.2   0.0131  0.907   1.984  1.177   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2420   0.2415
             R free    0.3169   0.3163
     Rms BondLength    0.0127   0.0131
      Rms BondAngle    1.9573   1.9835
     Rms ChirVolume    0.0866   0.0875
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      68.2s System:    0.2s Elapsed:     1:08