# Date 2008-01-16 Time 04:59:31 PST -0800 (1200488371.93 s)
#phil __OFF__

Command line arguments: "../546.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3790
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 546

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99062
Completeness in resolution range: 0.968075
Completeness with d_max=infinity: 0.965023

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9906

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99062
Completeness in resolution range: 0.968075
Completeness with d_max=infinity: 0.965023

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2589 [2136/2160]  1920   216  10.1%
  bin  2:  4.2589 -  3.3933 [2035/2054]  1836   199   9.8%
  bin  3:  3.3933 -  2.9682 [2017/2036]  1815   202  10.0%
  bin  4:  2.9682 -  2.6985 [1989/2019]  1783   206  10.4%
  bin  5:  2.6985 -  2.5061 [1997/2016]  1802   195   9.8%
  bin  6:  2.5061 -  2.3589 [1969/1994]  1773   196  10.0%
  bin  7:  2.3589 -  2.2412 [1961/1989]  1765   196  10.0%
  bin  8:  2.2412 -  2.1439 [1973/2009]  1774   199  10.1%
  bin  9:  2.1439 -  2.0616 [1924/1966]  1729   195  10.1%
  bin 10:  2.0616 -  1.9906 [1588/1992]  1433   155   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2191
        3.04 -     3.66: 4639
        3.66 -     4.28: 9017
        4.28 -     4.90: 12351
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.926 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.025 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.188 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28208 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001.geo

CPU time processing inputs: 9.69


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2402   r_free= 0.2357   ksol= 0.00   Bsol= 0.00   scale= 0.999    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.774010                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1385  153 0.2468 0.2479      6.2488      6.1881|
|  2:  4.7499 -  3.7902 0.99   1320  150 0.1782 0.1710      6.1102      6.1049|
|  3:  3.7902 -  3.3170 0.99   1311  144 0.2052 0.1947      6.0663      6.0643|
|  4:  3.3170 -  3.0165 0.99   1296  138 0.2123 0.2366      5.9407           6|
|  5:  3.0165 -  2.8018 0.99   1274  145 0.2418 0.2056      5.8235      5.7155|
|  6:  2.8018 -  2.6375 0.99   1294  148 0.2331 0.2556      5.7329      5.7166|
|  7:  2.6375 -  2.5061 0.99   1276  140 0.2428 0.2295      5.6986       5.697|
|  8:  2.5061 -  2.3974 0.98   1276  137 0.2587 0.2254      5.7215      5.6325|
|  9:  2.3974 -  2.3055 0.98   1249  144 0.2530 0.2550      5.6377      5.5855|
| 10:  2.3055 -  2.2262 0.99   1277  138 0.2635 0.2499       5.662      5.5574|
| 11:  2.2262 -  2.1568 0.98   1255  140 0.2650 0.2752      5.5882      5.6186|
| 12:  2.1568 -  2.0953 0.97   1251  140 0.2683 0.2621      5.5506      5.6587|
| 13:  2.0953 -  2.0403 1.00   1256  139 0.2779 0.2483      5.4829      5.4014|
| 14:  2.0403 -  1.9906 0.71    910  103 0.2652 0.2725      5.3833      5.3848|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1385   153  0.82  22.98   0.87     0.83      33749.61|
|  2:  4.7499 -  3.7902  1320   150  0.89  16.62   1.00     0.95      27244.99|
|  3:  3.7902 -  3.3170  1311   144  0.89  17.41   1.01     0.99      22010.52|
|  4:  3.3170 -  3.0165  1296   138  0.88  18.50   1.01     0.98      18473.07|
|  5:  3.0165 -  2.8018  1274   145  0.84  22.63   1.04     0.97      15087.27|
|  6:  2.8018 -  2.6375  1294   148  0.85  21.89   1.02     0.97      12946.85|
|  7:  2.6375 -  2.5061  1276   140  0.84  22.82   1.05     0.99      11819.92|
|  8:  2.5061 -  2.3974  1276   137  0.84  22.59   1.04     1.01      11223.07|
|  9:  2.3974 -  2.3055  1249   144  0.84  22.71   1.07     1.02      10534.54|
| 10:  2.3055 -  2.2262  1277   138  0.83  23.92   1.10     1.03       9977.40|
| 11:  2.2262 -  2.1568  1255   140  0.83  24.17   1.07     1.06       9920.06|
| 12:  2.1568 -  2.0953  1251   140  0.82  25.03   1.10     1.07       9658.27|
| 13:  2.0953 -  2.0403  1256   139  0.82  25.43   1.08     1.06       8589.61|
| 14:  2.0403 -  1.9906   910   103  0.82  25.36   1.10     1.01       6758.35|
|alpha:            min =        0.83 max =            1.07 mean =         0.99|
|beta:             min =     6758.35 max =        33749.61 mean =     15215.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           90.00 mean =        22.19|
|phase err.(test): min =        0.00 max =           89.86 mean =        22.02|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.639934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.715   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332871              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.360   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      184 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2007 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1827 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2812 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4635 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4382 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5631 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6720 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.160 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2402   r_free= 0.2357   ksol= 0.00   Bsol= 0.00   scale= 0.999    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.774010                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2210   r_free= 0.2177   ksol= 0.32   Bsol= 46.92   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.84,0.67,-0.00,0.00,0.00); trace/3= -1.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.729701                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.371585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.521   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191815              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.298   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2210      final r-factor (work) = 0.1402          |
| start r-factor (free) = 0.2177      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0030 = 2.37 * 0.50 * 5.7695 + 1.00 * 0.1616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4959 = 2.37 * 0.50 * 5.4289 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0477 = 0.19 * 1.00 * 5.4289 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0553 = 0.19 * 1.00 * 5.2283 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.49   16.24    None  None   None       |
|    all(noH): 2823   0      0.00    73.49   16.24    None  None   None       |
|    Sol.    : 438    0      7.31    62.64   36.95    None  None   None       |
|    Mac.    : 2385   0      0.00    73.49   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.349:  283   |   5:    36.745 -  44.094:  118        |
|      1:     7.349 -  14.698: 1577   |   6:    44.094 -  51.443:   82        |
|      2:    14.698 -  22.047:  451   |   7:    51.443 -  58.792:   52        |
|      3:    22.047 -  29.396:  138   |   8:    58.792 -  66.141:    8        |
|      4:    29.396 -  36.745:  113   |   9:    66.141 -  73.490:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1598             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1308 r_free = 0.1596             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1308   r_free= 0.1596   ksol= 0.32   Bsol= 46.92   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.84,0.67,-0.00,0.00,0.00); trace/3= -1.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.229409                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1580   ksol= 0.33   Bsol= 54.60   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.71,-0.76,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225451                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.500874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.956  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.641   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6005 = 2.50 * 0.50 * 5.2319 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5206 = 2.50 * 0.50 * 5.1609 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1496      final r-factor (free) = 0.1498          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5461 = 0.29 * 1.00 * 5.1609 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4759 = 0.29 * 1.00 * 5.1084 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    71.10   16.63    None  None   None       |
|    all(noH): 2823   0      1.30    71.10   16.63    None  None   None       |
|    Sol.    : 438    0      3.52    67.47   37.94    None  None   None       |
|    Mac.    : 2385   0      1.30    71.10   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.302 -   8.282:  573   |   5:    36.203 -  43.183:  112        |
|      1:     8.282 -  15.262: 1337   |   6:    43.183 -  50.163:   89        |
|      2:    15.262 -  22.242:  372   |   7:    50.163 -  57.144:   69        |
|      3:    22.242 -  29.223:  127   |   8:    57.144 -  64.124:   39        |
|      4:    29.223 -  36.203:   99   |   9:    64.124 -  71.104:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1101 r_free = 0.1498             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1498             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1498   ksol= 0.33   Bsol= 54.60   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.71,-0.76,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111391                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1497   ksol= 0.32   Bsol= 52.16   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.32,-0.77,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111122                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.051735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397729              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.121  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3088 = 2.05 * 0.50 * 5.1095 + 1.00 * 0.0672                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3017 = 2.05 * 0.50 * 5.1095 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0398 = 0.40 * 1.00 * 5.1095 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0412 = 0.40 * 1.00 * 5.1115 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    73.87   16.59    None  None   None       |
|    all(noH): 2823   0      0.76    73.87   16.59    None  None   None       |
|    Sol.    : 438    0      3.83    68.53   38.11    None  None   None       |
|    Mac.    : 2385   0      0.76    73.87   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.757 -   8.069:  582   |   5:    37.316 -  44.628:  118        |
|      1:     8.069 -  15.381: 1331   |   6:    44.628 -  51.940:   87        |
|      2:    15.381 -  22.692:  366   |   7:    51.940 -  59.251:   65        |
|      3:    22.692 -  30.004:  138   |   8:    59.251 -  66.563:   29        |
|      4:    30.004 -  37.316:  102   |   9:    66.563 -  73.875:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1529             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1529             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1529   ksol= 0.32   Bsol= 52.16   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.32,-0.77,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116568                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1529   ksol= 0.32   Bsol= 52.16   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.08,-0.64,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116580                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.960277              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.779  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.117498              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.209  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0709 = 1.96 * 0.50 * 5.1124 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0729 = 1.96 * 0.50 * 5.1161 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6093 = 0.12 * 1.00 * 5.1161 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6090 = 0.12 * 1.00 * 5.1284 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    70.60   15.95    None  None   None       |
|    all(noH): 2823   0      1.69    70.60   15.95    None  None   None       |
|    Sol.    : 438    0      6.03    67.39   35.58    None  None   None       |
|    Mac.    : 2385   0      1.69    70.60   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.693 -   8.584:  710   |   5:    36.148 -  43.039:  112        |
|      1:     8.584 -  15.475: 1238   |   6:    43.039 -  49.930:   85        |
|      2:    15.475 -  22.366:  356   |   7:    49.930 -  56.820:   47        |
|      3:    22.366 -  29.257:  123   |   8:    56.820 -  63.711:   21        |
|      4:    29.257 -  36.148:  128   |   9:    63.711 -  70.602:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1541             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1542             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1542   ksol= 0.32   Bsol= 52.16   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.08,-0.64,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127254                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1541   ksol= 0.32   Bsol= 52.16   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.01,-0.59,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127292                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.969216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 168.190  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.695  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6724 = 2.97 * 0.50 * 5.1286 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6660 = 2.97 * 0.50 * 5.1161 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4088 = 0.67 * 1.00 * 5.1161 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4037 = 0.67 * 1.00 * 5.1056 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.41    77.07   16.27    None  None   None       |
|    all(noH): 2823   0      0.41    77.07   16.27    None  None   None       |
|    Sol.    : 438    0      5.82    68.00   37.86    None  None   None       |
|    Mac.    : 2385   0      0.41    77.07   12.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.405 -   8.072:  647   |   5:    38.739 -  46.405:  112        |
|      1:     8.072 -  15.739: 1320   |   6:    46.405 -  54.072:   85        |
|      2:    15.739 -  23.405:  342   |   7:    54.072 -  61.739:   52        |
|      3:    23.405 -  31.072:  133   |   8:    61.739 -  69.405:   21        |
|      4:    31.072 -  38.739:  108   |   9:    69.405 -  77.072:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1062 r_free = 0.1544             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1061 r_free = 0.1544             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1544   ksol= 0.32   Bsol= 52.16   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.01,-0.59,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108141                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1385  153 0.1001 0.1300      5.4012       5.533|
|  2:  4.7499 -  3.7902 0.99   1320  150 0.0851 0.1136      5.4411      5.6457|
|  3:  3.7902 -  3.3170 0.99   1311  144 0.1013 0.1518      5.4514      5.8583|
|  4:  3.3170 -  3.0165 0.99   1296  138 0.1144 0.1466      5.4103      5.5334|
|  5:  3.0165 -  2.8018 0.99   1274  145 0.1246 0.1661       5.284      5.5275|
|  6:  2.8018 -  2.6375 0.99   1294  148 0.1146 0.1943      5.1774      5.4784|
|  7:  2.6375 -  2.5061 0.99   1276  140 0.1194 0.1522      5.1255      5.2869|
|  8:  2.5061 -  2.3974 0.98   1276  137 0.1068 0.1657      5.0215       5.317|
|  9:  2.3974 -  2.3055 0.98   1249  144 0.1082 0.1768      4.9794      5.2663|
| 10:  2.3055 -  2.2262 0.99   1277  138 0.1035 0.1629        4.91      5.1827|
| 11:  2.2262 -  2.1568 0.98   1255  140 0.1072 0.1703      4.9057      5.1885|
| 12:  2.1568 -  2.0953 0.97   1251  140 0.1069 0.1636      4.8409      5.2252|
| 13:  2.0953 -  2.0403 1.00   1256  139 0.1000 0.1689      4.7439      5.0119|
| 14:  2.0403 -  1.9906 0.71    910  103 0.0940 0.1680      4.6109       4.895|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1385   153  0.94   9.45   0.98     0.94       7499.25|
|  2:  4.7499 -  3.7902  1320   150  0.95   8.02   1.01     1.00       9267.99|
|  3:  3.7902 -  3.3170  1311   144  0.94  10.90   1.02     1.01      10040.37|
|  4:  3.3170 -  3.0165  1296   138  0.93  12.83   1.00     0.99       9533.40|
|  5:  3.0165 -  2.8018  1274   145  0.91  15.03   0.99     0.96       7700.06|
|  6:  2.8018 -  2.6375  1294   148  0.90  15.53   0.98     0.95       6738.60|
|  7:  2.6375 -  2.5061  1276   140  0.91  15.18   0.98     0.95       5852.28|
|  8:  2.5061 -  2.3974  1276   137  0.92  13.95   0.99     0.97       4872.39|
|  9:  2.3974 -  2.3055  1249   144  0.92  14.62   1.00     0.96       4610.49|
| 10:  2.3055 -  2.2262  1277   138  0.91  14.95   0.99     0.95       4029.15|
| 11:  2.2262 -  2.1568  1255   140  0.91  15.57   0.99     0.96       4217.42|
| 12:  2.1568 -  2.0953  1251   140  0.91  14.96   1.00     0.98       3725.22|
| 13:  2.0953 -  2.0403  1256   139  0.91  14.95   0.98     0.96       3160.55|
| 14:  2.0403 -  1.9906   910   103  0.92  13.74   0.96     0.92       2344.49|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2344.49 max =        10040.37 mean =      6086.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.49|
|phase err.(test): min =        0.00 max =           88.82 mean =        13.02|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1544   ksol= 0.32   Bsol= 52.15   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.73,-0.34,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108288                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1544   ksol= 0.32   Bsol= 52.15   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.73,-0.34,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108288                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1385  153 0.1001 0.1302      5.4021      5.5344|
|  2:  4.7499 -  3.7902 0.99   1320  150 0.0851 0.1136      5.4415      5.6454|
|  3:  3.7902 -  3.3170 0.99   1311  144 0.1014 0.1518      5.4513      5.8587|
|  4:  3.3170 -  3.0165 0.99   1296  138 0.1144 0.1466      5.4102      5.5335|
|  5:  3.0165 -  2.8018 0.99   1274  145 0.1246 0.1661      5.2839      5.5273|
|  6:  2.8018 -  2.6375 0.99   1294  148 0.1146 0.1944      5.1774      5.4785|
|  7:  2.6375 -  2.5061 0.99   1276  140 0.1194 0.1522      5.1257       5.287|
|  8:  2.5061 -  2.3974 0.98   1276  137 0.1068 0.1657      5.0216      5.3169|
|  9:  2.3974 -  2.3055 0.98   1249  144 0.1082 0.1768      4.9795      5.2662|
| 10:  2.3055 -  2.2262 0.99   1277  138 0.1035 0.1628      4.9101      5.1826|
| 11:  2.2262 -  2.1568 0.98   1255  140 0.1072 0.1702      4.9056      5.1882|
| 12:  2.1568 -  2.0953 0.97   1251  140 0.1069 0.1636      4.8408      5.2249|
| 13:  2.0953 -  2.0403 1.00   1256  139 0.1000 0.1690      4.7439       5.012|
| 14:  2.0403 -  1.9906 0.71    910  103 0.0941 0.1680      4.6113       4.895|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1385   153  0.94   9.46   0.98     0.95       7518.52|
|  2:  4.7499 -  3.7902  1320   150  0.95   8.03   1.01     1.00       9279.00|
|  3:  3.7902 -  3.3170  1311   144  0.94  10.90   1.02     1.01      10039.40|
|  4:  3.3170 -  3.0165  1296   138  0.93  12.83   1.01     0.99       9531.40|
|  5:  3.0165 -  2.8018  1274   145  0.91  15.03   1.00     0.97       7699.46|
|  6:  2.8018 -  2.6375  1294   148  0.90  15.54   0.99     0.96       6737.44|
|  7:  2.6375 -  2.5061  1276   140  0.91  15.18   0.99     0.96       5853.27|
|  8:  2.5061 -  2.3974  1276   137  0.92  13.95   1.00     0.98       4873.01|
|  9:  2.3974 -  2.3055  1249   144  0.92  14.63   1.01     0.97       4611.77|
| 10:  2.3055 -  2.2262  1277   138  0.91  14.95   1.00     0.96       4028.56|
| 11:  2.2262 -  2.1568  1255   140  0.91  15.57   1.00     0.97       4216.31|
| 12:  2.1568 -  2.0953  1251   140  0.91  14.95   1.01     1.00       3724.57|
| 13:  2.0953 -  2.0403  1256   139  0.91  14.95   1.00     0.98       3160.78|
| 14:  2.0403 -  1.9906   910   103  0.92  13.74   0.97     0.94       2345.77|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2345.77 max =        10039.40 mean =      6089.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.50|
|phase err.(test): min =        0.00 max =           88.82 mean =        13.02|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    77.06   16.26    None  None   None       |
|    all(noH): 2823   0      0.39    77.06   16.26    None  None   None       |
|    Sol.    : 438    0      5.81    67.99   37.84    None  None   None       |
|    Mac.    : 2385   0      0.39    77.06   12.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.393 -   8.060:  647   |   5:    38.726 -  46.393:  112        |
|      1:     8.060 -  15.726: 1320   |   6:    46.393 -  54.060:   85        |
|      2:    15.726 -  23.393:  342   |   7:    54.060 -  61.726:   52        |
|      3:    23.393 -  31.060:  133   |   8:    61.726 -  69.393:   21        |
|      4:    31.060 -  38.726:  108   |   9:    69.393 -  77.060:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.415 - 4.866
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 275
   mapped sites are within: 0.706 - 4.866

peak=    6.022 closest distance to " NH2 ARG A  56 " =    2.254
peak=    5.172 closest distance to " CG  PRO A  54 " =    1.259
peak=    5.147 closest distance to " CB  ARG A 275 " =    0.926
peak=    5.016 closest distance to " O   HOH Z 126 " =    1.884
peak=    4.981 closest distance to " CB  GLN A 223 " =    1.418
peak=    4.943 closest distance to " O   HOH Z 232 " =    2.408
peak=    4.879 closest distance to " NE2 GLN A  11 " =    1.087
peak=    4.776 closest distance to " CB  ARG A  79 " =    1.323
peak=    4.738 closest distance to " CB  GLN A 183 " =    1.229
peak=    4.707 closest distance to " CB  SER A  63 " =    1.141
peak=    4.666 closest distance to " CB  GLU A 152 " =    1.197
peak=    4.615 closest distance to " O   HOH Z 142 " =    1.631
peak=    4.554 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.539 closest distance to " O   HOH Z  15 " =    2.137
peak=    4.533 closest distance to " C   PRO A 198 " =    1.442
peak=    4.485 closest distance to " CB  ARG A 190 " =    1.691
peak=    4.436 closest distance to " O   HOH Z 236 " =    1.970
peak=    4.409 closest distance to " O   HOH Z 250 " =    1.518
peak=    4.386 closest distance to " O   HOH Z  78 " =    1.684
peak=    4.373 closest distance to " O   HOH Z 298 " =    1.848
peak=    4.363 closest distance to " O   HOH Z 303 " =    2.126
peak=    4.328 closest distance to " CG  PRO A 213 " =    1.175
peak=    4.320 closest distance to " O   HOH Z  61 " =    1.651
peak=    4.307 closest distance to " O   HOH Z 158 " =    3.023
peak=    4.287 closest distance to " O   HOH Z 369 " =    2.353
peak=    4.228 closest distance to " O   HOH Z 392 " =    3.058
peak=    4.214 closest distance to " O   HOH Z 427 " =    2.932
peak=    4.174 closest distance to " CB  PRO A  54 " =    0.904
peak=    4.158 closest distance to " CB  TYR A 169 " =    0.781
peak=    4.153 closest distance to " CD2 TRP A 179 " =    1.339
peak=    4.134 closest distance to " CB  ASN A 148 " =    1.694
peak=    4.128 closest distance to " O   HOH Z 346 " =    1.725
peak=    4.124 closest distance to " CB  TRP A 266 " =    1.001
peak=    4.119 closest distance to " O   HOH Z 189 " =    2.532
peak=    4.105 closest distance to " O   SER A  87 " =    2.256
peak=    4.104 closest distance to " CA  ASN A 215 " =    1.069
peak=    4.069 closest distance to " OD1 ASN A  69 " =    2.588
peak=    4.065 closest distance to " O   HOH Z 193 " =    1.911
peak=    4.063 closest distance to " CB  LEU A 228 " =    1.093
peak=    4.054 closest distance to " O   HOH Z  40 " =    1.753
peak=    4.035 closest distance to " O   HOH Z 234 " =    3.716
peak=    4.032 closest distance to " O   HOH Z  19 " =    2.442
peak=    4.024 closest distance to " CZ  PHE A 218 " =    1.101
peak=    4.016 closest distance to " O   HOH Z 209 " =    2.313
peak=    4.015 closest distance to " CE  LYS A  76 " =    0.878
peak=    4.001 closest distance to " ND2 ASN A 187 " =    1.469
peak=    3.996 closest distance to " CG2 VAL A 257 " =    0.874
peak=    3.989 closest distance to " O   HOH Z 423 " =    1.960
peak=    3.930 closest distance to " CD  ARG A 159 " =    0.712
peak=    3.912 closest distance to " O   HOH Z 313 " =    2.015
peak=    3.862 closest distance to " O   HOH Z  43 " =    1.869
peak=    3.860 closest distance to " O   HOH Z 403 " =    1.590
peak=    3.857 closest distance to " CA  TYR A  30 " =    1.033
peak=    3.848 closest distance to " NZ  LYS A 117 " =    3.274
peak=    3.841 closest distance to " O   HOH Z 389 " =    1.811
peak=    3.824 closest distance to " CB  VAL A 265 " =    1.252
peak=    3.823 closest distance to " O   HOH Z 128 " =    2.079
peak=    3.823 closest distance to " CB  ASP A 140 " =    1.008
peak=    3.818 closest distance to " OG ASER A 258 " =    3.096
peak=    3.812 closest distance to " O   HOH Z 203 " =    1.590
peak=    3.792 closest distance to " O   HOH Z 248 " =    1.582
peak=    3.784 closest distance to " CB  GLU A 277 " =    3.559
peak=    3.783 closest distance to " CA  ARG A  36 " =    1.005
peak=    3.783 closest distance to " O   HOH Z 180 " =    2.196
peak=    3.779 closest distance to " O   HOH Z 417 " =    3.335
peak=    3.778 closest distance to " CB  VAL A 202 " =    1.547
peak=    3.776 closest distance to " O   HOH Z 147 " =    1.804
peak=    3.738 closest distance to " O   HOH Z 272 " =    1.824
peak=    3.738 closest distance to " O   HOH Z 126 " =    2.045
peak=    3.733 closest distance to " O   HOH Z  10 " =    1.789
peak=    3.727 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.725 closest distance to " O   HOH Z 359 " =    1.530
peak=    3.712 closest distance to " O   HOH Z 265 " =    2.333
peak=    3.708 closest distance to " CG  PRO A 198 " =    1.239
peak=    3.697 closest distance to " O   HOH Z   1 " =    1.944
peak=    3.664 closest distance to " CB  ASN A  39 " =    0.893
peak=    3.662 closest distance to " O   HOH Z 245 " =    1.314
peak=    3.659 closest distance to " O   HOH Z 402 " =    1.386
peak=    3.657 closest distance to " CB  SER A   3 " =    1.282
peak=    3.652 closest distance to " O   HOH Z 261 " =    2.061
peak=    3.622 closest distance to " O  BHOH Z 338 " =    2.270
peak=    3.619 closest distance to " CG  PRO A  90 " =    1.166
peak=    3.616 closest distance to " CB  GLU A  46 " =    0.983
peak=    3.609 closest distance to " CD  ARG A  66 " =    2.538
peak=    3.591 closest distance to " O   HOH Z 291 " =    1.578
peak=    3.587 closest distance to " O   HOH Z 213 " =    1.809
peak=    3.586 closest distance to " N   ARG A 156 " =    1.354
peak=    3.583 closest distance to " O   HOH Z  97 " =    2.530
peak=    3.580 closest distance to " CG  PRO A 243 " =    1.002
peak=    3.579 closest distance to " CG2 ILE A 120 " =    1.082
peak=    3.566 closest distance to " CG2 ILE A  20 " =    1.313
peak=    3.562 closest distance to " O   HOH Z 368 " =    2.100
peak=    3.561 closest distance to " CG2AVAL A  72 " =    1.635
peak=    3.560 closest distance to " CB  ILE A 120 " =    1.294
peak=    3.558 closest distance to " O   HOH Z  21 " =    1.811
peak=    3.554 closest distance to " CB  ARG A 139 " =    1.038
peak=    3.554 closest distance to " O   HOH Z 148 " =    3.345
peak=    3.553 closest distance to " O   HOH Z 172 " =    3.365
peak=    3.550 closest distance to " O   HOH Z 280 " =    2.970
peak=    3.549 closest distance to " NH1AARG A 145 " =    1.229
peak=    3.548 closest distance to " CB  ALA A 291 " =    1.276
peak=    3.541 closest distance to " O   HOH Z  97 " =    1.965
peak=    3.538 closest distance to " O   HOH Z 425 " =    1.967
peak=    3.537 closest distance to " O   HOH Z 371 " =    3.093
peak=    3.535 closest distance to " CB  GLU A 128 " =    0.987
peak=    3.533 closest distance to " O   HOH Z 214 " =    2.113
peak=    3.529 closest distance to " O   HOH Z 344 " =    3.153
peak=    3.522 closest distance to " O   HOH Z 421 " =    1.879
peak=    3.521 closest distance to " O   HOH Z 305 " =    3.598
peak=    3.519 closest distance to " CB  THR A  31 " =    1.622
peak=    3.518 closest distance to " O   HOH Z 403 " =    1.415
peak=    3.512 closest distance to " OD2 ASP A 286 " =    2.824
peak=    3.510 closest distance to " OG BSER A 164 " =    2.333
peak=    3.507 closest distance to " CG  MET A 185 " =    1.094
peak=    3.505 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.500 closest distance to " O   HOH Z  54 " =    1.694
peak=    3.500 closest distance to " CA  ALA A  51 " =    0.900
peak=    3.499 closest distance to " NH2BARG A 145 " =    2.071
peak=    3.492 closest distance to " O   HOH Z 407 " =    2.361
peak=    3.490 closest distance to " NE2 GLN A  73 " =    3.917
peak=    3.489 closest distance to " O   HOH Z  66 " =    2.172
peak=    3.484 closest distance to " CA  ASP A 162 " =    1.032
peak=    3.483 closest distance to " O   HOH Z 175 " =    2.124
peak=    3.482 closest distance to " CB  ASN A 142 " =    1.048
peak=    3.477 closest distance to " O   MET A 105 " =    1.897
peak=    3.472 closest distance to " O   HOH Z  59 " =    1.995
peak=    3.471 closest distance to " CD1 LEU A 300 " =    1.224
peak=    3.470 closest distance to " CA  TYR A 116 " =    1.339
peak=    3.465 closest distance to " CB  SER A 212 " =    1.090
peak=    3.465 closest distance to " O   HOH Z 411 " =    3.913
peak=    3.464 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.462 closest distance to " CA  SER A  87 " =    1.001
peak=    3.457 closest distance to " CA  THR A 221 " =    1.030
peak=    3.456 closest distance to " OG1 THR A 294 " =    2.440
peak=    3.449 closest distance to " O   HOH Z  88 " =    3.028
peak=    3.443 closest distance to " O   HOH Z 261 " =    1.650
peak=    3.442 closest distance to " O   HOH Z 419 " =    2.017
peak=    3.438 closest distance to " OG BSER A  99 " =    2.309
peak=    3.434 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.430 closest distance to " CG1 ILE A  33 " =    1.228
peak=    3.430 closest distance to " O   HOH Z 368 " =    3.576
peak=    3.427 closest distance to " CD1 ILE A 106 " =    0.777
peak=    3.427 closest distance to " O   HOH Z 234 " =    1.940
peak=    3.409 closest distance to " CG1 VAL A 153 " =    1.028
peak=    3.409 closest distance to " O   ASN A  74 " =    1.534
peak=    3.409 closest distance to " O   HOH Z 299 " =    4.438
peak=    3.407 closest distance to " O   HOH Z 337 " =    3.624
peak=    3.406 closest distance to " O   HOH Z 188 " =    2.079
peak=    3.406 closest distance to " O   HOH Z  44 " =    1.684
peak=    3.405 closest distance to " CA  THR A 264 " =    0.902
peak=    3.399 closest distance to " NH2 ARG A 156 " =    1.178
peak=    3.396 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.394 closest distance to " CZ2 TRP A 179 " =    1.763
peak=    3.393 closest distance to " O   HOH Z 185 " =    1.831
peak=    3.389 closest distance to " CD2 LEU A 297 " =    0.812
peak=    3.389 closest distance to " OG  SER A  22 " =    2.635
peak=    3.383 closest distance to " O   HOH Z 128 " =    2.265
peak=    3.379 closest distance to " O   HOH Z 173 " =    1.890
peak=    3.376 closest distance to " CA  ALA A  84 " =    1.207
peak=    3.376 closest distance to " CB  PHE A 204 " =    0.706
peak=    3.375 closest distance to " O   HOH Z 302 " =    2.086
peak=    3.374 closest distance to " CD  LYS A 166 " =    1.232
peak=    3.373 closest distance to " NE2 HIS A 207 " =    1.296
peak=    3.371 closest distance to " CA  ALA A 291 " =    0.824
peak=    3.361 closest distance to " O   HOH Z 193 " =    2.106
peak=    3.361 closest distance to " CD BLYS A 290 " =    0.981
peak=    3.359 closest distance to " O   HOH Z 353 " =    2.647
peak=    3.353 closest distance to " O   HOH Z 258 " =    1.636
peak=    3.352 closest distance to " CA  MET A 105 " =    1.010
peak=    3.348 closest distance to " CG1 ILE A  49 " =    1.487
peak=    3.347 closest distance to " CB  ASN A 224 " =    1.024
peak=    3.341 closest distance to " N   ASN A  39 " =    1.259
peak=    3.340 closest distance to " NE2 GLN A  77 " =    3.160
peak=    3.338 closest distance to " O   HOH Z 133 " =    2.628
peak=    3.333 closest distance to " O   HOH Z  88 " =    2.498
peak=    3.331 closest distance to " CB  TYR A 116 " =    0.746
peak=    3.325 closest distance to " CE1 TYR A 186 " =    1.325
peak=    3.322 closest distance to " N   TYR A 116 " =    1.538
peak=    3.315 closest distance to " O   HOH Z 132 " =    2.628
peak=    3.314 closest distance to " O   ALA A   1 " =    1.656
peak=    3.314 closest distance to " O   HOH Z 383 " =    1.849
peak=    3.308 closest distance to " O   HOH Z 273 " =    2.837
peak=    3.308 closest distance to " CB  ASN A 215 " =    1.155
peak=    3.296 closest distance to " O   HOH Z 325 " =    2.501
peak=    3.295 closest distance to " CG2 ILE A 234 " =    0.814
peak=    3.293 closest distance to " CG  LYS A  76 " =    0.938
peak=    3.290 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.288 closest distance to " CA  ALA A 158 " =    1.299
peak=    3.287 closest distance to " CB  ALA A   9 " =    1.532
peak=    3.283 closest distance to " NZ  LYS A  48 " =    1.234
peak=    3.270 closest distance to " CG  LEU A 167 " =    1.287
peak=    3.268 closest distance to " N   PHE A 130 " =    1.323
peak=    3.267 closest distance to " CB  LYS A 290 " =    1.023
peak=    3.265 closest distance to " O   HOH Z 345 " =    3.295
peak=    3.260 closest distance to " O   HOH Z 329 " =    4.042
peak=    3.258 closest distance to " O   ALA A 165 " =    1.526
peak=    3.256 closest distance to " CA  PHE A 283 " =    1.344
peak=    3.250 closest distance to " O   HOH Z 285 " =    2.647
peak=    3.249 closest distance to " CB  SER A 141 " =    0.989
peak=    3.247 closest distance to " OE1 GLU A   2 " =    2.195
peak=    3.245 closest distance to " CD  ARG A 269 " =    0.931
peak=    3.240 closest distance to " O   HOH Z 426 " =    1.646
peak=    3.239 closest distance to " CA  ASN A 217 " =    1.184
peak=    3.235 closest distance to " O   HOH Z  44 " =    3.060
peak=    3.231 closest distance to " CA  ARG A 159 " =    1.246
peak=    3.225 closest distance to " O   HOH Z 365 " =    2.895
peak=    3.223 closest distance to " CB  VAL A 126 " =    1.068
peak=    3.216 closest distance to " CA  ALA A 233 " =    1.260
peak=    3.215 closest distance to " CB  ALA A   1 " =    4.866
peak=    3.213 closest distance to " O   HOH Z 298 " =    2.476
peak=    3.210 closest distance to " CD1 LEU A  96 " =    0.731
peak=    3.209 closest distance to " O   HOH Z 371 " =    1.693
peak=    3.209 closest distance to " CB  ALA A 114 " =    1.120
peak=    3.209 closest distance to " CZ  PHE A  38 " =    1.275
peak=    3.208 closest distance to " CG  GLN A  11 " =    1.582
peak=    3.208 closest distance to " ND2 ASN A 249 " =    0.877
peak=    3.207 closest distance to " CE BLYS A 290 " =    1.135
peak=    3.203 closest distance to " N   ASN A 127 " =    1.265
peak=    3.199 closest distance to " O   HOH Z 116 " =    1.770
peak=    3.198 closest distance to " CB  PRO A  90 " =    1.180
peak=    3.197 closest distance to " O   THR A 220 " =    1.290
peak=    3.197 closest distance to " CG2 THR A 221 " =    1.072
peak=    3.195 closest distance to " CG BARG A 275 " =    1.444
peak=    3.195 closest distance to " CD  LYS A  76 " =    1.733
peak=    3.192 closest distance to " CB  THR A 157 " =    1.136
peak=    3.192 closest distance to " O   HOH Z  61 " =    1.420
peak=    3.192 closest distance to " CD  ARG A  66 " =    2.431
peak=    3.191 closest distance to " CB  GLN A  89 " =    1.370
peak=    3.190 closest distance to " CB  ASP A 298 " =    1.156
peak=    3.187 closest distance to " O   HOH Z  88 " =    1.990
peak=    3.186 closest distance to " CG1 VAL A 189 " =    2.076
peak=    3.182 closest distance to " O   HOH Z 271 " =    2.279
peak=    3.176 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.173 closest distance to " O   HOH Z 371 " =    3.372
peak=    3.172 closest distance to " ND2 ASN A 110 " =    1.613
peak=    3.172 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.168 closest distance to " CD1 ILE A 263 " =    1.284
peak=    3.166 closest distance to " CD  LYS A 119 " =    1.393
peak=    3.161 closest distance to " CB  ALA A  34 " =    1.013
peak=    3.160 closest distance to " O   HOH Z 433 " =    1.761
peak=    3.158 closest distance to " NE AARG A 190 " =    2.032
peak=    3.155 closest distance to " O   HOH Z 325 " =    3.960
peak=    3.151 closest distance to " O   HOH Z 409 " =    3.113
peak=    3.143 closest distance to " CA  VAL A 125 " =    1.098
peak=    3.139 closest distance to " O   HOH Z 336 " =    1.696
peak=    3.137 closest distance to " CB  ALA A 248 " =    0.877
peak=    3.134 closest distance to " CB  MET A  47 " =    1.201
peak=    3.134 closest distance to " O   HOH Z 193 " =    1.635
peak=    3.133 closest distance to " CG  GLU A  37 " =    0.823
peak=    3.131 closest distance to " O   HOH Z 411 " =    1.719
peak=    3.130 closest distance to " O   HOH Z  85 " =    1.997
peak=    3.124 closest distance to " O   HOH Z 258 " =    2.071
peak=    3.120 closest distance to " CD  GLN A 194 " =    1.384
peak=    3.118 closest distance to " ND1 HIS A  86 " =    1.642
peak=    3.118 closest distance to " CG  GLN A  77 " =    2.050
peak=    3.117 closest distance to " O   HOH Z 130 " =    2.167
peak=    3.111 closest distance to " O   HOH Z 391 " =    2.904
peak=    3.102 closest distance to " CA  ASN A 252 " =    1.751
peak=    3.097 closest distance to " N   ASP A 162 " =    1.183
peak=    3.093 closest distance to " CA  ALA A 248 " =    1.103
peak=    3.088 closest distance to " O   HOH Z 219 " =    1.781
peak=    3.082 closest distance to " O   HOH Z 171 " =    3.958
peak=    3.077 closest distance to " CB  GLU A 236 " =    1.021
peak=    3.071 closest distance to " N   SER A 135 " =    1.244
peak=    3.068 closest distance to " O   TRP A 274 " =    1.823
peak=    3.067 closest distance to " N   GLY A  98 " =    1.049
peak=    3.056 closest distance to " O   HOH Z  96 " =    1.886
peak=    3.043 closest distance to " ND1 HIS A  81 " =    1.693
peak=    3.010 closest distance to " O   SER A 164 " =    1.172

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.765 - 5.255
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.765 - 5.255

peak=   -4.774 closest distance to " CD  GLN A  58 " =    0.994
peak=   -4.663 closest distance to " O   HOH Z 266 " =    5.226
peak=   -4.631 closest distance to " O   VAL A  67 " =    2.721
peak=   -4.618 closest distance to " CB  PRO A 243 " =    2.658
peak=   -4.556 closest distance to " SG  CYS A 254 " =    3.520
peak=   -4.479 closest distance to " CG1 VAL A 112 " =    2.612
peak=   -4.447 closest distance to " CD  ARG A 156 " =    2.092
peak=   -4.348 closest distance to " C   HIS A 108 " =    1.120
peak=   -4.314 closest distance to " OG BSER A 134 " =    1.281
peak=   -4.245 closest distance to " CG1 VAL A 112 " =    2.807
peak=   -4.229 closest distance to " CD2 PHE A 192 " =    2.039
peak=   -4.173 closest distance to " O   HOH Z 198 " =    2.040
peak=   -4.166 closest distance to " O   HOH Z 372 " =    2.287
peak=   -4.154 closest distance to " O   HOH Z 377 " =    2.186
peak=   -4.134 closest distance to " O   HOH Z 231 " =    2.242
peak=   -4.106 closest distance to " CG  GLN A 223 " =    2.003
peak=   -4.101 closest distance to " CZ3 TRP A 179 " =    1.157
peak=   -4.041 closest distance to " CA  VAL A  67 " =    2.873
peak=   -3.945 closest distance to " O   HOH Z 389 " =    1.885
peak=   -3.937 closest distance to " O   HOH Z  73 " =    2.294
peak=   -3.923 closest distance to " CE  MET A 105 " =    2.481
peak=   -3.919 closest distance to " OD1 ASP A 171 " =    1.661
peak=   -3.917 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.914 closest distance to " O   ILE A 109 " =    2.571
peak=   -3.894 closest distance to " CB  ALA A  43 " =    2.493
peak=   -3.891 closest distance to " O   HOH Z 114 " =    3.118
peak=   -3.856 closest distance to " ND2 ASN A  45 " =    1.739
peak=   -3.835 closest distance to " CB  ALA A 291 " =    2.435
peak=   -3.820 closest distance to " O   HOH Z 196 " =    2.030
peak=   -3.820 closest distance to " CG2 ILE A 263 " =    2.320
peak=   -3.808 closest distance to " O   HOH Z 407 " =    3.027
peak=   -3.794 closest distance to " OG  SER A  97 " =    2.243
peak=   -3.791 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.780 closest distance to " O   HOH Z 211 " =    1.630
peak=   -3.779 closest distance to " CD1 LEU A 101 " =    2.314
peak=   -3.765 closest distance to " O   PRO A 163 " =    2.106
peak=   -3.761 closest distance to " CD  ARG A 139 " =    1.569
peak=   -3.760 closest distance to " O   HOH Z  10 " =    1.475
peak=   -3.755 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -3.736 closest distance to " OXT GLY A 302 " =    2.773
peak=   -3.726 closest distance to " N   ALA A  43 " =    2.609
peak=   -3.723 closest distance to " O   HOH Z 313 " =    1.920
peak=   -3.703 closest distance to " CB  ASP A 132 " =    2.309
peak=   -3.686 closest distance to " O   HOH Z 290 " =    1.362
peak=   -3.686 closest distance to " O   HOH Z 435 " =    2.848
peak=   -3.682 closest distance to " CA  GLY A 203 " =    2.351
peak=   -3.668 closest distance to " O   HOH Z 185 " =    2.311
peak=   -3.666 closest distance to " CD1 PHE A  59 " =    1.972
peak=   -3.662 closest distance to " CB  ASN A  39 " =    2.353
peak=   -3.646 closest distance to " CB  ALA A 248 " =    2.302
peak=   -3.636 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.629 closest distance to " CG  ARG A 269 " =    2.364
peak=   -3.620 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.609 closest distance to " CG  ARG A  66 " =    2.420
peak=   -3.600 closest distance to " NH2AARG A 275 " =    5.255
peak=   -3.598 closest distance to " OD2 ASP A 191 " =    1.468
peak=   -3.577 closest distance to " CG  PHE A 283 " =    2.623
peak=   -3.573 closest distance to " CB  ALA A 248 " =    2.200
peak=   -3.568 closest distance to " CA  ASP A 298 " =    1.091
peak=   -3.568 closest distance to " O   HOH Z 198 " =    1.380
peak=   -3.561 closest distance to " ND2 ASN A 187 " =    1.492
peak=   -3.545 closest distance to " CD2 PHE A  61 " =    2.568
peak=   -3.536 closest distance to " NE2 GLN A  88 " =    1.810
peak=   -3.523 closest distance to " N   SER A 212 " =    2.039
peak=   -3.519 closest distance to " O   HOH Z 394 " =    1.459
peak=   -3.518 closest distance to " O   HOH Z 311 " =    3.729
peak=   -3.512 closest distance to " ND2 ASN A 249 " =    2.172
peak=   -3.507 closest distance to " O   HOH Z  44 " =    2.282
peak=   -3.507 closest distance to " O   HOH Z 126 " =    1.928
peak=   -3.500 closest distance to " CZ  TYR A 169 " =    1.782
peak=   -3.497 closest distance to " CZ  PHE A 155 " =    1.263
peak=   -3.497 closest distance to " N   ALA A 248 " =    1.700
peak=   -3.492 closest distance to " CE2 PHE A 218 " =    2.433
peak=   -3.489 closest distance to " NE2 GLN A 278 " =    1.764
peak=   -3.484 closest distance to " ND2 ASN A  45 " =    1.196
peak=   -3.477 closest distance to " CG1 VAL A 250 " =    2.669
peak=   -3.476 closest distance to " O   HOH Z 353 " =    2.133
peak=   -3.472 closest distance to " O   VAL A 189 " =    2.666
peak=   -3.461 closest distance to " OD2 ASP A 171 " =    2.428
peak=   -3.456 closest distance to " CD2 TYR A 293 " =    2.068
peak=   -3.456 closest distance to " CD  ARG A 195 " =    5.215
peak=   -3.452 closest distance to " NE2 GLN A 194 " =    1.817
peak=   -3.451 closest distance to " O   PHE A 218 " =    1.578
peak=   -3.442 closest distance to " O   HOH Z  51 " =    1.713
peak=   -3.417 closest distance to " O   HOH Z  38 " =    1.576
peak=   -3.417 closest distance to " O   HOH Z  13 " =    1.596
peak=   -3.415 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.410 closest distance to " O   ALA A  10 " =    1.704
peak=   -3.404 closest distance to " CB  ASP A 286 " =    2.059
peak=   -3.399 closest distance to " CB  TRP A  85 " =    2.593
peak=   -3.395 closest distance to " O   ALA A 161 " =    1.751
peak=   -3.389 closest distance to " O   HOH Z 243 " =    1.849
peak=   -3.384 closest distance to " O   HOH Z 253 " =    3.896
peak=   -3.382 closest distance to " CA  GLY A 133 " =    2.000
peak=   -3.380 closest distance to " O   HOH Z  11 " =    1.696
peak=   -3.373 closest distance to " O   HOH Z 298 " =    1.250
peak=   -3.354 closest distance to " CE BMET A  47 " =    1.564
peak=   -3.354 closest distance to " OH  TYR A 247 " =    2.071
peak=   -3.349 closest distance to " CG  GLU A 277 " =    1.200
peak=   -3.349 closest distance to " O   HOH Z 134 " =    3.042
peak=   -3.347 closest distance to " SG ACYS A 201 " =    1.939
peak=   -3.334 closest distance to " C   LEU A 143 " =    1.013
peak=   -3.333 closest distance to " O   HOH Z  43 " =    1.662
peak=   -3.332 closest distance to " CA  GLY A 241 " =    3.118
peak=   -3.331 closest distance to " O   SER A  95 " =    1.557
peak=   -3.331 closest distance to " NH2 ARG A  79 " =    1.564
peak=   -3.327 closest distance to " CZ  PHE A 192 " =    2.869
peak=   -3.324 closest distance to " O   HOH Z 166 " =    1.966
peak=   -3.323 closest distance to " CB  PRO A 163 " =    2.498
peak=   -3.315 closest distance to " O   PRO A 198 " =    1.316
peak=   -3.314 closest distance to " O   HOH Z 317 " =    1.516
peak=   -3.312 closest distance to " CD1 LEU A   5 " =    2.524
peak=   -3.310 closest distance to " C   ALA A 158 " =    1.353
peak=   -3.304 closest distance to " NH2BARG A 275 " =    2.000
peak=   -3.302 closest distance to " CB  TYR A  15 " =    2.169
peak=   -3.296 closest distance to " O   HOH Z 357 " =    2.078
peak=   -3.295 closest distance to " O   HOH Z 177 " =    1.733
peak=   -3.295 closest distance to " CG1 VAL A 230 " =    2.073
peak=   -3.294 closest distance to " CG1 VAL A 197 " =    2.267
peak=   -3.288 closest distance to " O   LYS A 117 " =    1.754
peak=   -3.284 closest distance to " N   THR A 157 " =    1.579
peak=   -3.283 closest distance to " O   HOH Z 295 " =    1.631
peak=   -3.282 closest distance to " CD  GLN A 223 " =    0.950
peak=   -3.281 closest distance to " O   VAL A 174 " =    2.090
peak=   -3.278 closest distance to " O   SER A 135 " =    1.479
peak=   -3.277 closest distance to " OG BSER A 134 " =    1.767
peak=   -3.275 closest distance to " CD1 LEU A 228 " =    2.169
peak=   -3.275 closest distance to " OG  SER A  62 " =    1.672
peak=   -3.270 closest distance to " O   PRO A  90 " =    1.792
peak=   -3.270 closest distance to " OD1 ASN A 187 " =    1.669
peak=   -3.269 closest distance to " CD2 LEU A 237 " =    2.701
peak=   -3.267 closest distance to " O   HOH Z 123 " =    2.325
peak=   -3.261 closest distance to " O   LEU A 101 " =    2.704
peak=   -3.260 closest distance to " C   MET A 188 " =    1.310
peak=   -3.258 closest distance to " CB  PHE A 208 " =    2.270
peak=   -3.257 closest distance to " CD1 LEU A  83 " =    2.688
peak=   -3.252 closest distance to " CG2 VAL A 189 " =    2.101
peak=   -3.252 closest distance to " C   PRO A  90 " =    1.499
peak=   -3.246 closest distance to " O   HOH Z   6 " =    1.397
peak=   -3.246 closest distance to " CG1 VAL A 125 " =    2.375
peak=   -3.245 closest distance to " CB  SER A 245 " =    2.199
peak=   -3.244 closest distance to " CD1 ILE A 239 " =    2.375
peak=   -3.242 closest distance to " CG  PRO A 163 " =    2.567
peak=   -3.242 closest distance to " O   HOH Z 421 " =    3.084
peak=   -3.239 closest distance to " O   HOH Z 292 " =    4.568
peak=   -3.236 closest distance to " CG  GLU A 152 " =    1.290
peak=   -3.235 closest distance to " CD1 ILE A 151 " =    2.430
peak=   -3.231 closest distance to " O   HOH Z  71 " =    2.041
peak=   -3.226 closest distance to " CA  GLY A 241 " =    2.301
peak=   -3.226 closest distance to " NE2 GLN A  11 " =    1.801
peak=   -3.222 closest distance to " O   HOH Z 207 " =    2.181
peak=   -3.211 closest distance to " O   HOH Z 174 " =    4.206
peak=   -3.208 closest distance to " O   HOH Z  60 " =    2.166
peak=   -3.203 closest distance to " NH2 ARG A  79 " =    2.028
peak=   -3.202 closest distance to " O   HOH Z 174 " =    2.565
peak=   -3.201 closest distance to " OE2 GLU A 152 " =    1.239
peak=   -3.200 closest distance to " O   HOH Z  41 " =    2.407
peak=   -3.183 closest distance to " CD2 HIS A 207 " =    2.444
peak=   -3.182 closest distance to " O   ALA A  51 " =    1.286
peak=   -3.179 closest distance to " OE2 GLU A   2 " =    1.951
peak=   -3.177 closest distance to " O   GLY A  80 " =    2.538
peak=   -3.173 closest distance to " CG  ASN A 252 " =    1.693
peak=   -3.167 closest distance to " OE1 GLN A 223 " =    1.922
peak=   -3.160 closest distance to " CG1 VAL A  67 " =    3.080
peak=   -3.157 closest distance to " O   HOH Z  37 " =    1.740
peak=   -3.150 closest distance to " O   HOH Z 108 " =    2.440
peak=   -3.146 closest distance to " O   HOH Z  63 " =    1.736
peak=   -3.143 closest distance to " C   GLN A  58 " =    1.977
peak=   -3.142 closest distance to " NH1 ARG A  36 " =    2.063
peak=   -3.137 closest distance to " O   ARG A 145 " =    1.531
peak=   -3.132 closest distance to " O   HOH Z 377 " =    1.767
peak=   -3.125 closest distance to " CG1 VAL A 125 " =    1.947
peak=   -3.124 closest distance to " O   HOH Z 266 " =    5.070
peak=   -3.122 closest distance to " CE3 TRP A 274 " =    2.458
peak=   -3.117 closest distance to " CG  LEU A  83 " =    1.912
peak=   -3.110 closest distance to " CG2 THR A 221 " =    2.220
peak=   -3.108 closest distance to " CG  TRP A 266 " =    1.939
peak=   -3.108 closest distance to " CA  GLY A 241 " =    2.836
peak=   -3.105 closest distance to " O   HOH Z 339 " =    1.819
peak=   -3.096 closest distance to " O   GLN A 240 " =    2.032
peak=   -3.087 closest distance to " O   HOH Z 265 " =    1.814
peak=   -3.084 closest distance to " CD1 TRP A  70 " =    1.061
peak=   -3.077 closest distance to " CG1AVAL A  41 " =    2.878
peak=   -3.071 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.069 closest distance to " O   GLN A 240 " =    2.446
peak=   -3.068 closest distance to " ND2 ASN A  60 " =    1.400
peak=   -3.063 closest distance to " O   ASN A 301 " =    1.517
peak=   -3.062 closest distance to " O   HOH Z 216 " =    1.420
peak=   -3.059 closest distance to " OD2 ASP A 171 " =    1.840
peak=   -3.048 closest distance to " NH1 ARG A 195 " =    2.587
peak=   -3.039 closest distance to " CG2AVAL A  72 " =    2.837
peak=   -3.034 closest distance to " CE  LYS A  76 " =    2.788
peak=   -3.018 closest distance to " OD1AASN A 224 " =    1.757

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.2402 0.2357   5.774010e+00   5.749534e+00
   1_bss:  0.2210 0.2177   5.729701e+00   5.700233e+00
   1_xyz:  0.1402 0.1599   5.279115e+00   5.385595e+00
   1_adp:  0.1312 0.1598   5.230983e+00   5.395572e+00
   1_occ:  0.1308 0.1596   5.229409e+00   5.395572e+00
   2_bss:  0.1304 0.1580   5.225451e+00   5.387741e+00
   2_xyz:  0.1153 0.1496   5.134047e+00   5.338241e+00
   2_adp:  0.1101 0.1498   5.111663e+00   5.340912e+00
   2_occ:  0.1100 0.1498   5.111391e+00   5.340966e+00
   3_bss:  0.1098 0.1497   5.111122e+00   5.340779e+00
   3_xyz:  0.1093 0.1518   5.115728e+00   5.354196e+00
   3_adp:  0.1088 0.1529   5.116351e+00   5.360749e+00
   3_occ:  0.1087 0.1529   5.116568e+00   5.361201e+00
   4_bss:  0.1086 0.1529   5.116580e+00   5.361120e+00
   4_xyz:  0.1086 0.1543   5.120420e+00   5.369808e+00
   4_adp:  0.1104 0.1541   5.126890e+00   5.368260e+00
   4_occ:  0.1103 0.1542   5.127254e+00   5.369014e+00
   5_bss:  0.1103 0.1541   5.127292e+00   5.369029e+00
   5_xyz:  0.1077 0.1542   5.113977e+00   5.365971e+00
   5_adp:  0.1062 0.1544   5.108123e+00   5.366851e+00
   5_occ:  0.1061 0.1544   5.108141e+00   5.366941e+00
   5_bss:  0.1060 0.1544   5.108288e+00   5.366999e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.319  46.920  -2.936  -2.836   0.667  -0.000   0.000   0.000
   1_xyz:  0.319  46.920  -2.936  -2.836   0.667  -0.000   0.000   0.000
   1_adp:  0.319  46.920  -2.936  -2.836   0.667  -0.000   0.000   0.000
   1_occ:  0.319  46.920  -2.936  -2.836   0.667  -0.000   0.000   0.000
   2_bss:  0.327  54.600  -3.149  -2.714  -0.759  -0.000  -0.000  -0.000
   2_xyz:  0.327  54.600  -3.149  -2.714  -0.759  -0.000  -0.000  -0.000
   2_adp:  0.327  54.600  -3.149  -2.714  -0.759  -0.000  -0.000  -0.000
   2_occ:  0.327  54.600  -3.149  -2.714  -0.759  -0.000  -0.000  -0.000
   3_bss:  0.324  52.165  -2.787  -2.325  -0.775  -0.000  -0.000  -0.000
   3_xyz:  0.324  52.165  -2.787  -2.325  -0.775  -0.000  -0.000  -0.000
   3_adp:  0.324  52.165  -2.787  -2.325  -0.775  -0.000  -0.000  -0.000
   3_occ:  0.324  52.165  -2.787  -2.325  -0.775  -0.000  -0.000  -0.000
   4_bss:  0.321  52.165  -2.552  -2.083  -0.639  -0.000  -0.000  -0.000
   4_xyz:  0.321  52.165  -2.552  -2.083  -0.639  -0.000  -0.000  -0.000
   4_adp:  0.321  52.165  -2.552  -2.083  -0.639  -0.000  -0.000  -0.000
   4_occ:  0.321  52.165  -2.552  -2.083  -0.639  -0.000  -0.000  -0.000
   5_bss:  0.321  52.165  -2.476  -2.005  -0.590  -0.000  -0.000  -0.000
   5_xyz:  0.321  52.165  -2.476  -2.005  -0.590  -0.000  -0.000  -0.000
   5_adp:  0.321  52.165  -2.476  -2.005  -0.590  -0.000  -0.000  -0.000
   5_occ:  0.321  52.165  -2.476  -2.005  -0.590  -0.000  -0.000  -0.000
   5_bss:  0.321  52.150  -2.189  -1.730  -0.340  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  22.175 0.8445  0.9937    15214.692
   1_bss:  20.652 0.8577  0.9508    12267.522
   1_xyz:  13.987 0.9155  0.9911     6433.870
   1_adp:  14.207 0.9134  0.9865     6523.124
   1_occ:  14.212 0.9133  0.9862     6514.119
   2_bss:  14.043 0.9147  0.9695     6426.595
   2_xyz:  12.953 0.9234  0.9711     5739.354
   2_adp:  13.036 0.9226  0.9655     5706.279
   2_occ:  13.036 0.9226  0.9653     5705.132
   3_bss:  13.034 0.9227  0.9740     5705.948
   3_xyz:  13.216 0.9214  0.9740     5918.962
   3_adp:  13.346 0.9205  0.9673     5982.365
   3_occ:  13.358 0.9204  0.9672     5987.765
   4_bss:  13.358 0.9204  0.9743     5987.364
   4_xyz:  13.502 0.9193  0.9738     6092.066
   4_adp:  13.430 0.9199  0.9688     6100.120
   4_occ:  13.446 0.9198  0.9687     6108.090
   5_bss:  13.446 0.9198  0.9710     6108.761
   5_xyz:  13.393 0.9201  0.9718     6109.679
   5_adp:  13.446 0.9197  0.9652     6085.170
   5_occ:  13.447 0.9197  0.9651     6086.327
   5_bss:  13.449 0.9197  0.9741     6088.441
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6160e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6160e-01
   1_xyz:   0.986  0.007  0.071 15.156  0.004  4.115   5.8356e-02
   1_adp:   0.986  0.007  0.071 15.156  0.004  4.115   5.8356e-02
   1_occ:   0.986  0.007  0.071 15.156  0.004  4.115   5.8356e-02
   2_bss:   0.986  0.007  0.071 15.156  0.004  4.115   5.8356e-02
   2_xyz:   1.051  0.009  0.080 14.892  0.004  4.120   6.7176e-02
   2_adp:   1.051  0.009  0.080 14.892  0.004  4.120   6.7176e-02
   2_occ:   1.051  0.009  0.080 14.892  0.004  4.120   6.7176e-02
   3_bss:   1.051  0.009  0.080 14.892  0.004  4.120   6.7176e-02
   3_xyz:   0.992  0.008  0.078 14.659  0.004  4.116   6.0052e-02
   3_adp:   0.992  0.008  0.078 14.659  0.004  4.116   6.0052e-02
   3_occ:   0.992  0.008  0.078 14.659  0.004  4.116   6.0052e-02
   4_bss:   0.992  0.008  0.078 14.659  0.004  4.116   6.0052e-02
   4_xyz:   0.978  0.007  0.077 14.535  0.004  4.117   5.8435e-02
   4_adp:   0.978  0.007  0.077 14.535  0.004  4.117   5.8435e-02
   4_occ:   0.978  0.007  0.077 14.535  0.004  4.117   5.8435e-02
   5_bss:   0.978  0.007  0.077 14.535  0.004  4.117   5.8435e-02
   5_xyz:   1.072  0.010  0.084 14.783  0.004  4.118   7.0534e-02
   5_adp:   1.072  0.010  0.084 14.783  0.004  4.118   7.0534e-02
   5_occ:   1.072  0.010  0.084 14.783  0.004  4.118   7.0534e-02
   5_bss:   1.072  0.010  0.084 14.783  0.004  4.118   7.0534e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_xyz:   6.867  0.047  0.254 82.380  0.034  2.280   4.4168e-02
   1_adp:   6.867  0.047  0.254 82.380  0.034  2.280   4.4168e-02
   1_occ:   6.867  0.047  0.254 82.380  0.034  2.280   4.4168e-02
   2_bss:   6.867  0.047  0.254 82.380  0.034  2.280   4.4168e-02
   2_xyz:   6.836  0.046  0.283 83.463  0.039  2.319   5.1398e-02
   2_adp:   6.836  0.046  0.283 83.463  0.039  2.319   5.1398e-02
   2_occ:   6.836  0.046  0.283 83.463  0.039  2.319   5.1398e-02
   3_bss:   6.836  0.046  0.283 83.463  0.039  2.319   5.1398e-02
   3_xyz:   6.780  0.047  0.255 83.264  0.038  2.358   4.2480e-02
   3_adp:   6.780  0.047  0.255 83.264  0.038  2.358   4.2480e-02
   3_occ:   6.780  0.047  0.255 83.264  0.038  2.358   4.2480e-02
   4_bss:   6.780  0.047  0.255 83.264  0.038  2.358   4.2480e-02
   4_xyz:   6.656  0.047  0.247 82.870  0.036  2.343   3.9737e-02
   4_adp:   6.656  0.047  0.247 82.870  0.036  2.343   3.9737e-02
   4_occ:   6.656  0.047  0.247 82.870  0.036  2.343   3.9737e-02
   5_bss:   6.656  0.047  0.247 82.870  0.036  2.343   3.9737e-02
   5_xyz:   7.181  0.055  0.281 83.641  0.036  2.252   5.6219e-02
   5_adp:   7.181  0.055  0.281 83.641  0.036  2.252   5.6219e-02
   5_occ:   7.181  0.055  0.281 83.641  0.036  2.252   5.6219e-02
   5_bss:   7.181  0.055  0.281 83.641  0.036  2.252   5.6219e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  73.49   0.00  16.24  73.49   0.00  12.43  62.64   7.31  36.95
   1_occ:  73.49   0.00  16.24  73.49   0.00  12.43  62.64   7.31  36.95
   2_bss:  73.49   0.00  16.24  73.49   0.00  12.43  62.64   7.31  36.95
   2_xyz:  73.49   0.00  16.24  73.49   0.00  12.43  62.64   7.31  36.95
   2_adp:  71.10   1.30  16.63  71.10   1.30  12.72  67.47   3.52  37.94
   2_occ:  71.10   1.30  16.63  71.10   1.30  12.72  67.47   3.52  37.94
   3_bss:  71.10   1.30  16.63  71.10   1.30  12.72  67.47   3.52  37.94
   3_xyz:  71.10   1.30  16.63  71.10   1.30  12.72  67.47   3.52  37.94
   3_adp:  73.87   0.76  16.59  73.87   0.76  12.64  68.53   3.83  38.11
   3_occ:  73.87   0.76  16.59  73.87   0.76  12.64  68.53   3.83  38.11
   4_bss:  73.87   0.76  16.59  73.87   0.76  12.64  68.53   3.83  38.11
   4_xyz:  73.87   0.76  16.59  73.87   0.76  12.64  68.53   3.83  38.11
   4_adp:  70.60   1.69  15.95  70.60   1.69  12.35  67.39   6.03  35.58
   4_occ:  70.60   1.69  15.95  70.60   1.69  12.35  67.39   6.03  35.58
   5_bss:  70.60   1.69  15.95  70.60   1.69  12.35  67.39   6.03  35.58
   5_xyz:  70.60   1.69  15.95  70.60   1.69  12.35  67.39   6.03  35.58
   5_adp:  77.07   0.41  16.27  77.07   0.41  12.31  68.00   5.82  37.86
   5_occ:  77.07   0.41  16.27  77.07   0.41  12.31  68.00   5.82  37.86
   5_bss:  77.06   0.39  16.26  77.06   0.39  12.29  67.99   5.81  37.84
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.627    0.009    0.192
   1_adp:    0.627    0.009    0.192
   1_occ:    0.627    0.009    0.192
   2_bss:    0.627    0.009    0.192
   2_xyz:    0.841    0.012    0.226
   2_adp:    0.841    0.012    0.226
   2_occ:    0.841    0.012    0.226
   3_bss:    0.841    0.012    0.226
   3_xyz:    1.150    0.011    0.233
   3_adp:    1.150    0.011    0.233
   3_occ:    1.150    0.011    0.233
   4_bss:    1.150    0.011    0.233
   4_xyz:    1.219    0.013    0.239
   4_adp:    1.219    0.013    0.239
   4_occ:    1.219    0.013    0.239
   5_bss:    1.219    0.013    0.239
   5_xyz:    1.221    0.012    0.241
   5_adp:    1.221    0.012    0.241
   5_occ:    1.221    0.012    0.241
   5_bss:    1.221    0.012    0.241
------------------------------------------------------------------------

CPU time actual refinement: 313.95


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_546/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 313.80 
  Macro-tasks:
    bulk solvent and scale       = 38.37  
    individual site refinement   = 124.34 
    weights calculation          = 29.40  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 198.75 
  Micro-tasks:
    mask                            = 0.60   
    f_calc                          = 98.84  
    alpha_beta                      = 7.90   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 107.19 
    fmodel                         = 6.42   
    r_factors                      = 0.18   
    phase_errors                   = 10.94  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 233.45 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.530 micro seconds
Total CPU time: 5.46 minutes
from_scatterers_fft:    632 calls, 98.62 s
gradients_fft:          577 calls, 94.30 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 05:04:58 PST -0800 (1200488698.21 s)
Start R-work = 0.2402, R-free = 0.2357 (no bulk solvent and anisotropic scale)
Final R-work = 0.1289, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.2210, R-free = 0.2177
Final R-work = 0.1060, R-free = 0.1544