# Date 2008-01-16 Time 04:43:01 PST -0800 (1200487381.59 s)
#phil __OFF__

Command line arguments: "../428.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30894
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 428

-------------------------------------------------------------------------------
  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: (69.5475, 46.93, 88.5498, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (69.5475, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98082
Completeness in resolution range: 0.944594
Completeness with d_max=infinity: 0.941688

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9808

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: (69.5475, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98082
Completeness in resolution range: 0.944594
Completeness with d_max=infinity: 0.941688

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2384 [2183/2210]  1963   220  10.1%
  bin  2:  4.2384 -  3.3768 [2088/2104]  1879   209  10.0%
  bin  3:  3.3768 -  2.9536 [2063/2082]  1859   204   9.9%
  bin  4:  2.9536 -  2.6853 [2051/2081]  1843   208  10.1%
  bin  5:  2.6853 -  2.4938 [2029/2048]  1827   202  10.0%
  bin  6:  2.4938 -  2.3473 [2018/2043]  1815   203  10.1%
  bin  7:  2.3473 -  2.2302 [2019/2053]  1825   194   9.6%
  bin  8:  2.2302 -  2.1334 [2010/2040]  1798   212  10.5%
  bin  9:  2.1334 -  2.0514 [1994/2036]  1799   195   9.8%
  bin 10:  2.0514 -  1.9808 [1134/2041]  1022   112   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/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: 0.14 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:
        1.32 -     2.04: 12
        2.04 -     2.75: 350
        2.75 -     3.47: 4550
        3.47 -     4.18: 9306
        4.18 -     4.90: 13914
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.324 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.427 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.574 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.751 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.756 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28127 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_428/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 69.5475 46.93 88.54975 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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3816   r_free= 0.3757   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.172367                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.3070 0.3044      6.4403      6.3673|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.3058 0.3367      6.6033      6.7101|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.3560 0.3090      6.5483      6.4617|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.3606 0.3888      6.3758        6.42|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.3952 0.3518      6.2466      6.2024|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.4071 0.4481      6.1505      6.1529|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.4023 0.3492      6.1183      5.9988|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.4294 0.3835      6.1085      6.0449|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.4265 0.4307      6.0272      6.0849|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.4409 0.4401      6.0431      5.9982|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.4419 0.4183      5.9571       5.933|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.4458 0.4345      5.8864      5.9489|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.4432 0.4937      5.8284      5.8179|
| 14:  2.0302 -  1.9808 0.42    537   69 0.3833 0.3527      5.7616      5.6413|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1415   157  0.78  26.67   0.85     0.80      46092.51|
|  2:  4.7272 -  3.7718  1364   151  0.80  26.51   0.95     0.88      65173.29|
|  3:  3.7718 -  3.3008  1331   149  0.73  32.54   0.94     0.89      67629.99|
|  4:  3.3008 -  3.0017  1331   144  0.68  37.30   0.95     0.83      60176.91|
|  5:  3.0017 -  2.7880  1311   151  0.62  42.33   0.95     0.78      48444.38|
|  6:  2.7880 -  2.6246  1328   145  0.60  44.26   0.94     0.77      43286.73|
|  7:  2.6246 -  2.4938  1291   146  0.61  42.82   0.97     0.79      37971.91|
|  8:  2.4938 -  2.3856  1295   141  0.61  43.12   0.96     0.79      33320.16|
|  9:  2.3856 -  2.2941  1317   146  0.61  43.77   0.97     0.80      31570.99|
| 10:  2.2941 -  2.2152  1280   139  0.59  45.24   1.00     0.78      29875.50|
| 11:  2.2152 -  2.1462  1294   154  0.55  47.96   0.97     0.81      31740.55|
| 12:  2.1462 -  2.0850  1281   131  0.54  49.04   0.98     0.79      28938.30|
| 13:  2.0850 -  2.0302  1255   136  0.52  50.40   0.98     0.77      26308.37|
| 14:  2.0302 -  1.9808   537    69  0.56  47.94   1.05     0.71      21012.60|
|alpha:            min =        0.71 max =            0.89 mean =         0.80|
|beta:             min =    21012.60 max =        67629.99 mean =     41954.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           90.00 mean =        40.94|
|phase err.(test): min =        0.00 max =           89.76 mean =        40.73|
|-----------------------------------------------------------------------------|

============================== 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 = 6.764162              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.371   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.929821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.069   (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 |  1.324 -  1.682:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.682 -  2.039:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.039 -  2.397:       11 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.397 -  2.755:      339 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.755 -  3.112:     2254 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.112 -  3.470:     2296 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.470 -  3.827:     4327 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.827 -  4.185:     4979 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.185 -  4.542:     6266 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.542 -  4.900:     7648 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.324 |       0.413 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3816   r_free= 0.3757   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.172367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3647   r_free= 0.3593   ksol= 0.31   Bsol= 41.61   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-3.03,6.07,-0.00,0.00,0.00); trace/3= 0.23                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.147714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.838281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.082   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.526127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.833   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3647      final r-factor (work) = 0.2378          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1245 = 5.84 * 0.50 * 6.1474 + 1.00 * 0.1794                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3526 = 5.84 * 0.50 * 5.9102 + 1.00 * 0.0999                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2378      final r-factor (work) = 0.2160          |
| start r-factor (free) = 0.2629      final r-factor (free) = 0.2722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1159 = 0.53 * 1.00 * 5.9102 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0080 = 0.53 * 1.00 * 5.6954 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.64   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    78.64   17.70    None  None   None       |
|    Sol.    : 438    0      3.89    78.64   40.51    None  None   None       |
|    Mac.    : 2385   0      0.00    70.84   13.52    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 -   7.864:  573   |   5:    39.319 -  47.183:  111        |
|      1:     7.864 -  15.728: 1187   |   6:    47.183 -  55.047:   86        |
|      2:    15.728 -  23.592:  456   |   7:    55.047 -  62.911:   56        |
|      3:    23.592 -  31.456:  188   |   8:    62.911 -  70.775:   24        |
|      4:    31.456 -  39.319:  128   |   9:    70.775 -  78.639:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2160 r_free = 0.2722             target_work(ml) = 5.709         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2157 r_free = 0.2724             target_work(ml) = 5.709         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2157   r_free= 0.2724   ksol= 0.31   Bsol= 41.61   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-3.03,6.07,-0.00,0.00,0.00); trace/3= 0.23                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.709206                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2105   r_free= 0.2692   ksol= 0.31   Bsol= 58.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.63,1.29,-0.00,0.00,0.00); trace/3= -1.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.694964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.495426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.167   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243086              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.540  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2105      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.2692      final r-factor (free) = 0.1988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8999 = 4.50 * 0.50 * 5.6947 + 1.00 * 0.0999                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5780 = 4.50 * 0.50 * 5.5655 + 1.00 * 0.0683                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1495      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3644 = 0.24 * 1.00 * 5.5655 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3109 = 0.24 * 1.00 * 5.3576 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    77.26   17.13    None  None   None       |
|    all(noH): 2823   0      1.07    77.26   17.13    None  None   None       |
|    Sol.    : 438    0      5.95    77.26   39.98    None  None   None       |
|    Mac.    : 2385   0      1.07    71.87   12.94    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:     1.066 -   8.685:  688   |   5:    39.161 -  46.780:  101        |
|      1:     8.685 -  16.304: 1260   |   6:    46.780 -  54.399:  102        |
|      2:    16.304 -  23.923:  346   |   7:    54.399 -  62.018:   50        |
|      3:    23.923 -  31.542:  132   |   8:    62.018 -  69.637:   22        |
|      4:    31.542 -  39.161:  111   |   9:    69.637 -  77.256:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1833             target_work(ml) = 5.316         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1379 r_free = 0.1831             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1831   ksol= 0.31   Bsol= 58.07   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.63,1.29,-0.00,0.00,0.00); trace/3= -1.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.315139                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1816   ksol= 0.33   Bsol= 63.16   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.43,0.09,-0.00,0.00,0.00); trace/3= -1.78                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.310585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.624750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.157  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.647184              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.033  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1376      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1816      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7776 = 3.62 * 0.50 * 5.3572 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5931 = 3.62 * 0.50 * 5.2521 + 1.00 * 0.0744                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4075 = 0.65 * 1.00 * 5.2521 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3624 = 0.65 * 1.00 * 5.1803 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.02    87.68   17.29    None  None   None       |
|    all(noH): 2823   0      1.02    87.68   17.29    None  None   None       |
|    Sol.    : 438    0      5.40    87.68   41.16    None  None   None       |
|    Mac.    : 2385   0      1.02    82.15   12.91    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:     1.025 -   9.690:  983   |   5:    44.353 -  53.018:   92        |
|      1:     9.690 -  18.356: 1123   |   6:    53.018 -  61.684:   83        |
|      2:    18.356 -  27.021:  248   |   7:    61.684 -  70.349:   40        |
|      3:    27.021 -  35.687:  127   |   8:    70.349 -  79.015:   12        |
|      4:    35.687 -  44.353:  110   |   9:    79.015 -  87.680:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1628             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1629             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1629   ksol= 0.33   Bsol= 63.16   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.43,0.09,-0.00,0.00,0.00); trace/3= -1.78                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177164                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1629   ksol= 0.33   Bsol= 63.16   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.21,-0.12,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.169739              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.726  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6947 = 2.17 * 0.50 * 5.1802 + 1.00 * 0.0748                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6767 = 2.17 * 0.50 * 5.1762 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2526 = 0.24 * 1.00 * 5.1762 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2506 = 0.24 * 1.00 * 5.1725 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    86.61   16.82    None  None   None       |
|    all(noH): 2823   0      1.50    86.61   16.82    None  None   None       |
|    Sol.    : 438    0      1.70    86.61   39.35    None  None   None       |
|    Mac.    : 2385   0      1.50    81.89   12.68    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:     1.499 -  10.010: 1076   |   5:    44.055 -  52.566:   92        |
|      1:    10.010 -  18.521: 1051   |   6:    52.566 -  61.077:   70        |
|      2:    18.521 -  27.032:  243   |   7:    61.077 -  69.588:   32        |
|      3:    27.032 -  35.543:  122   |   8:    69.588 -  78.099:   10        |
|      4:    35.543 -  44.055:  122   |   9:    78.099 -  86.610:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1596             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1596             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1596   ksol= 0.33   Bsol= 63.16   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.21,-0.12,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1586   ksol= 0.33   Bsol= 63.16   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.12,-0.18,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.168367                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.457119              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.151  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.582843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8295 = 1.46 * 0.50 * 5.1723 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8214 = 1.46 * 0.50 * 5.1727 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0234 = 0.58 * 1.00 * 5.1727 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0239 = 0.58 * 1.00 * 5.1719 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    89.67   16.79    None  None   None       |
|    all(noH): 2823   0      0.77    89.67   16.79    None  None   None       |
|    Sol.    : 438    0      2.97    89.67   39.71    None  None   None       |
|    Mac.    : 2385   0      0.77    84.47   12.58    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:     0.769 -   9.659: 1033   |   5:    45.218 -  54.108:   95        |
|      1:     9.659 -  18.549: 1097   |   6:    54.108 -  62.998:   63        |
|      2:    18.549 -  27.439:  238   |   7:    62.998 -  71.888:   30        |
|      3:    27.439 -  36.328:  133   |   8:    71.888 -  80.778:   11        |
|      4:    36.328 -  45.218:  120   |   9:    80.778 -  89.668:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1605             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1604             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1604   ksol= 0.33   Bsol= 63.16   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.12,-0.18,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176090                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.1009 0.1295      5.4135      5.5564|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.0874 0.1071      5.4493       5.622|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.1085 0.1549      5.4859      5.8426|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.1233 0.1581      5.4545      5.6179|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.1344 0.1591      5.3429      5.5165|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.1280 0.2042      5.2369      5.5311|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.1330 0.1717      5.2136      5.3706|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.1177 0.1694       5.112       5.341|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.1211 0.1984      5.0516      5.3863|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.1177 0.1628      4.9821      5.1577|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.1193 0.1925      4.9553      5.3224|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.1223 0.1630      4.9379      5.1944|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.1107 0.1907      4.8062       5.064|
| 14:  2.0302 -  1.9808 0.42    537   69 0.0915 0.1715      4.6379      4.9606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1415   157  0.94   9.39   0.97     0.94       7549.25|
|  2:  4.7272 -  3.7718  1364   151  0.95   7.99   1.00     0.99       9095.83|
|  3:  3.7718 -  3.3008  1331   149  0.93  11.47   1.02     1.02      10321.54|
|  4:  3.3008 -  3.0017  1331   144  0.92  13.41   1.00     1.00      10186.03|
|  5:  3.0017 -  2.7880  1311   151  0.90  15.95   0.99     0.97       8592.45|
|  6:  2.7880 -  2.6246  1328   145  0.89  17.17   0.97     0.95       7511.31|
|  7:  2.6246 -  2.4938  1291   146  0.90  16.20   0.98     0.94       6739.88|
|  8:  2.4938 -  2.3856  1295   141  0.90  15.96   0.99     0.96       5928.54|
|  9:  2.3856 -  2.2941  1317   146  0.90  16.30   0.99     0.94       5217.96|
| 10:  2.2941 -  2.2152  1280   139  0.90  16.21   0.99     0.96       4629.05|
| 11:  2.2152 -  2.1462  1294   154  0.90  16.75   0.98     0.94       4529.75|
| 12:  2.1462 -  2.0850  1281   131  0.90  17.00   0.99     0.98       4471.89|
| 13:  2.0850 -  2.0302  1255   136  0.90  16.87   0.97     0.95       3583.77|
| 14:  2.0302 -  1.9808   537    69  0.93  13.15   0.96     0.92       2468.05|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2468.05 max =        10321.54 mean =      6705.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.55|
|phase err.(test): min =        0.00 max =           89.70 mean =        14.06|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1603   ksol= 0.33   Bsol= 63.13   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.92,-0.03,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176201                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1603   ksol= 0.33   Bsol= 63.13   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.92,-0.03,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176201                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1415  157 0.1009 0.1296      5.4141      5.5576|
|  2:  4.7272 -  3.7718 0.99   1364  151 0.0875 0.1072      5.4496      5.6219|
|  3:  3.7718 -  3.3008 0.99   1331  149 0.1085 0.1550      5.4859      5.8429|
|  4:  3.3008 -  3.0017 0.99   1331  144 0.1233 0.1581      5.4545      5.6181|
|  5:  3.0017 -  2.7880 0.99   1311  151 0.1343 0.1590      5.3429      5.5163|
|  6:  2.7880 -  2.6246 0.99   1328  145 0.1280 0.2042       5.237      5.5314|
|  7:  2.6246 -  2.4938 0.99   1291  146 0.1330 0.1716      5.2137      5.3705|
|  8:  2.4938 -  2.3856 0.98   1295  141 0.1177 0.1694      5.1122       5.341|
|  9:  2.3856 -  2.2941 0.98   1317  146 0.1211 0.1984      5.0517      5.3863|
| 10:  2.2941 -  2.2152 0.98   1280  139 0.1177 0.1627      4.9822      5.1575|
| 11:  2.2152 -  2.1462 0.99   1294  154 0.1193 0.1924      4.9552       5.322|
| 12:  2.1462 -  2.0850 0.97   1281  131 0.1223 0.1630      4.9378      5.1945|
| 13:  2.0850 -  2.0302 0.95   1255  136 0.1107 0.1909      4.8062      5.0644|
| 14:  2.0302 -  1.9808 0.42    537   69 0.0915 0.1714      4.6383      4.9604|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7272  1415   157  0.94   9.41   0.97     0.94       7560.59|
|  2:  4.7272 -  3.7718  1364   151  0.95   8.00   1.01     0.99       9102.23|
|  3:  3.7718 -  3.3008  1331   149  0.93  11.47   1.02     1.02      10324.06|
|  4:  3.3008 -  3.0017  1331   144  0.92  13.42   1.01     1.00      10187.56|
|  5:  3.0017 -  2.7880  1311   151  0.90  15.95   1.00     0.97       8594.91|
|  6:  2.7880 -  2.6246  1328   145  0.89  17.17   0.98     0.95       7510.76|
|  7:  2.6246 -  2.4938  1291   146  0.90  16.20   0.99     0.95       6740.64|
|  8:  2.4938 -  2.3856  1295   141  0.90  15.97   1.00     0.96       5930.98|
|  9:  2.3856 -  2.2941  1317   146  0.90  16.30   0.99     0.95       5217.98|
| 10:  2.2941 -  2.2152  1280   139  0.90  16.21   1.00     0.96       4628.19|
| 11:  2.2152 -  2.1462  1294   154  0.90  16.74   0.98     0.94       4526.18|
| 12:  2.1462 -  2.0850  1281   131  0.90  17.00   0.99     0.99       4471.77|
| 13:  2.0850 -  2.0302  1255   136  0.90  16.87   0.98     0.96       3582.81|
| 14:  2.0302 -  1.9808   537    69  0.93  13.15   0.97     0.93       2468.00|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2468.00 max =        10324.06 mean =      6706.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.55|
|phase err.(test): min =        0.00 max =           89.70 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.974)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    89.64   16.76    None  None   None       |
|    all(noH): 2823   0      0.74    89.64   16.76    None  None   None       |
|    Sol.    : 438    0      2.95    89.64   39.68    None  None   None       |
|    Mac.    : 2385   0      0.74    84.45   12.55    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:     0.743 -   9.633: 1033   |   5:    45.192 -  54.082:   95        |
|      1:     9.633 -  18.523: 1097   |   6:    54.082 -  62.972:   63        |
|      2:    18.523 -  27.413:  238   |   7:    62.972 -  71.862:   30        |
|      3:    27.413 -  36.303:  133   |   8:    71.862 -  80.752:   11        |
|      4:    36.303 -  45.192:  120   |   9:    80.752 -  89.642:    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)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.505 - 5.327
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 281
   mapped sites are within: 0.703 - 5.327

peak=    5.291 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.178 closest distance to " CG  PRO A  54 " =    1.429
peak=    5.057 closest distance to " CZ  PHE A 218 " =    1.108
peak=    4.996 closest distance to " CB  ARG A 275 " =    0.956
peak=    4.950 closest distance to " O   HOH Z 113 " =    2.124
peak=    4.839 closest distance to " O   HOH Z 232 " =    2.351
peak=    4.817 closest distance to " NE2 GLN A  11 " =    1.140
peak=    4.783 closest distance to " CG  PRO A  90 " =    1.224
peak=    4.687 closest distance to " CB  PRO A  54 " =    1.014
peak=    4.665 closest distance to " CG  PRO A 198 " =    1.281
peak=    4.651 closest distance to " O   HOH Z 142 " =    1.768
peak=    4.621 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.610 closest distance to " O   HOH Z 298 " =    1.917
peak=    4.597 closest distance to " O   HOH Z 369 " =    2.229
peak=    4.550 closest distance to " O   HOH Z 188 " =    2.952
peak=    4.490 closest distance to " CB  ARG A 190 " =    1.606
peak=    4.483 closest distance to " CG  PRO A 243 " =    1.070
peak=    4.475 closest distance to " O   HOH Z 126 " =    1.905
peak=    4.430 closest distance to " ND2 ASN A 187 " =    1.543
peak=    4.406 closest distance to " O   HOH Z 265 " =    2.094
peak=    4.406 closest distance to " CB  VAL A 265 " =    1.262
peak=    4.316 closest distance to " CB  ARG A  79 " =    1.375
peak=    4.315 closest distance to " CG2 VAL A 257 " =    0.830
peak=    4.300 closest distance to " CG  PRO A 213 " =    1.240
peak=    4.285 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.277 closest distance to " O  BHOH Z  74 " =    1.231
peak=    4.264 closest distance to " CZ3 TRP A 266 " =    1.112
peak=    4.238 closest distance to " ND2 ASN A 249 " =    0.892
peak=    4.236 closest distance to " CD2 TRP A 179 " =    1.301
peak=    4.231 closest distance to " O   HOH Z 406 " =    1.684
peak=    4.230 closest distance to " O   HOH Z  19 " =    2.457
peak=    4.191 closest distance to " CB  PRO A  90 " =    1.082
peak=    4.176 closest distance to " CB  ASN A 148 " =    1.507
peak=    4.168 closest distance to " O   HOH Z 287 " =    1.911
peak=    4.130 closest distance to " CE  LYS A  76 " =    0.923
peak=    4.119 closest distance to " CB  SER A  63 " =    1.153
peak=    4.113 closest distance to " CZ  PHE A  38 " =    1.282
peak=    4.103 closest distance to " O   HOH Z 313 " =    2.059
peak=    4.094 closest distance to " O   HOH Z 303 " =    2.179
peak=    4.074 closest distance to " CA  ARG A  36 " =    1.050
peak=    4.074 closest distance to " CB  ARG A  79 " =    0.942
peak=    4.064 closest distance to " CB  GLU A 152 " =    1.211
peak=    4.054 closest distance to " O   HOH Z 250 " =    1.516
peak=    4.051 closest distance to " O   ASN A  74 " =    1.350
peak=    4.047 closest distance to " CB  ASN A  39 " =    0.890
peak=    4.044 closest distance to " O  BHOH Z 338 " =    2.297
peak=    4.041 closest distance to " CB  ASN A 142 " =    1.040
peak=    4.030 closest distance to " O   HOH Z  78 " =    1.636
peak=    4.028 closest distance to " O   SER A  87 " =    2.280
peak=    4.026 closest distance to " CD  ARG A 269 " =    0.970
peak=    4.012 closest distance to " CA  ASN A 215 " =    1.016
peak=    3.999 closest distance to " O   HOH Z  15 " =    2.263
peak=    3.987 closest distance to " N   ASN A  39 " =    1.257
peak=    3.987 closest distance to " O   HOH Z 214 " =    2.134
peak=    3.980 closest distance to " CB  GLU A 277 " =    3.689
peak=    3.962 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.941 closest distance to " CG2 ILE A 120 " =    1.190
peak=    3.929 closest distance to " O   HOH Z  40 " =    1.820
peak=    3.922 closest distance to " CA  ARG A 195 " =    1.215
peak=    3.921 closest distance to " O   HOH Z  43 " =    1.986
peak=    3.916 closest distance to " O   HOH Z 261 " =    2.084
peak=    3.913 closest distance to " CA  ASN A 127 " =    1.188
peak=    3.889 closest distance to " CB  VAL A 202 " =    1.538
peak=    3.888 closest distance to " CB  ASN A 110 " =    1.128
peak=    3.884 closest distance to " O   HOH Z 427 " =    3.052
peak=    3.869 closest distance to " CG  MET A 185 " =    1.150
peak=    3.863 closest distance to " O   HOH Z 158 " =    3.124
peak=    3.863 closest distance to " NZ  LYS A 117 " =    3.121
peak=    3.840 closest distance to " CB  ASP A 124 " =    0.760
peak=    3.832 closest distance to " CB  GLU A  46 " =    1.008
peak=    3.818 closest distance to " CA  THR A 264 " =    0.961
peak=    3.817 closest distance to " CG  GLU A  37 " =    0.972
peak=    3.816 closest distance to " N   TYR A 116 " =    1.500
peak=    3.807 closest distance to " CB  LEU A 228 " =    1.093
peak=    3.796 closest distance to " O   PRO A 198 " =    1.588
peak=    3.770 closest distance to " O   THR A 220 " =    1.235
peak=    3.769 closest distance to " O   HOH Z 353 " =    2.646
peak=    3.763 closest distance to " NH1AARG A 145 " =    1.278
peak=    3.752 closest distance to " O   HOH Z  63 " =    1.908
peak=    3.750 closest distance to " CB  SER A 210 " =    0.779
peak=    3.745 closest distance to " O   HOH Z 180 " =    2.219
peak=    3.745 closest distance to " O   HOH Z 327 " =    1.522
peak=    3.739 closest distance to " O   HOH Z 126 " =    1.526
peak=    3.739 closest distance to " CB  ASN A 187 " =    1.416
peak=    3.736 closest distance to " CB  GLU A 128 " =    0.933
peak=    3.730 closest distance to " CG  GLN A  11 " =    1.973
peak=    3.725 closest distance to " CD  ARG A 159 " =    0.717
peak=    3.725 closest distance to " CA  ILE A 234 " =    1.040
peak=    3.706 closest distance to " O   HOH Z 403 " =    1.597
peak=    3.704 closest distance to " OG ASER A 258 " =    3.119
peak=    3.699 closest distance to " CB  THR A  31 " =    1.546
peak=    3.692 closest distance to " O   HOH Z 132 " =    2.943
peak=    3.683 closest distance to " O   HOH Z  61 " =    1.738
peak=    3.674 closest distance to " CG  LEU A 167 " =    1.232
peak=    3.673 closest distance to " O   HOH Z 234 " =    3.719
peak=    3.673 closest distance to " O   ASN A  74 " =    2.086
peak=    3.672 closest distance to " O   THR A 182 " =    1.413
peak=    3.667 closest distance to " CA  ALA A 154 " =    1.044
peak=    3.667 closest distance to " CA  SER A  87 " =    1.028
peak=    3.662 closest distance to " O   HOH Z 346 " =    1.662
peak=    3.657 closest distance to " OG BSER A 164 " =    2.325
peak=    3.653 closest distance to " O   HOH Z 248 " =    1.604
peak=    3.652 closest distance to " CG AARG A 275 " =    1.177
peak=    3.649 closest distance to " OG BSER A 134 " =    2.798
peak=    3.647 closest distance to " CG  ARG A  66 " =    2.402
peak=    3.647 closest distance to " O   HOH Z 368 " =    2.137
peak=    3.633 closest distance to " O   HOH Z 251 " =    1.646
peak=    3.633 closest distance to " N   ARG A 156 " =    1.360
peak=    3.627 closest distance to " O   HOH Z 402 " =    1.362
peak=    3.623 closest distance to " CD1 ILE A 199 " =    1.114
peak=    3.618 closest distance to " NE2 HIS A 207 " =    1.130
peak=    3.605 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.603 closest distance to " CB  LEU A  83 " =    0.742
peak=    3.602 closest distance to " CD1 LEU A  96 " =    0.747
peak=    3.600 closest distance to " NE  ARG A  56 " =    3.525
peak=    3.597 closest distance to " CB  PHE A 204 " =    0.822
peak=    3.593 closest distance to " O   HOH Z 411 " =    3.952
peak=    3.591 closest distance to " O   HOH Z 423 " =    1.963
peak=    3.588 closest distance to " O   HOH Z 163 " =    1.986
peak=    3.581 closest distance to " O   HOH Z 337 " =    3.610
peak=    3.564 closest distance to " CB  ASP A 140 " =    1.091
peak=    3.564 closest distance to " CD  LYS A 166 " =    1.252
peak=    3.554 closest distance to " O   HOH Z 128 " =    2.050
peak=    3.550 closest distance to " CG2AVAL A  72 " =    1.750
peak=    3.548 closest distance to " CA  ALA A 160 " =    0.929
peak=    3.548 closest distance to " CA  ALA A  51 " =    0.892
peak=    3.548 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.548 closest distance to " O   HOH Z 368 " =    3.653
peak=    3.546 closest distance to " O   HOH Z  57 " =    2.190
peak=    3.546 closest distance to " O   HOH Z 209 " =    2.236
peak=    3.536 closest distance to " O   HOH Z 359 " =    1.676
peak=    3.535 closest distance to " O   HOH Z 203 " =    1.677
peak=    3.535 closest distance to " CA  GLN A  94 " =    0.779
peak=    3.531 closest distance to " CA  ARG A 139 " =    0.937
peak=    3.496 closest distance to " CG2AVAL A 121 " =    2.335
peak=    3.490 closest distance to " CA  VAL A 125 " =    1.130
peak=    3.487 closest distance to " O   HOH Z 172 " =    3.695
peak=    3.486 closest distance to " O   HOH Z 291 " =    1.523
peak=    3.480 closest distance to " O   HOH Z 285 " =    2.143
peak=    3.478 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.475 closest distance to " CB  GLN A  89 " =    1.376
peak=    3.475 closest distance to " O   HOH Z 394 " =    3.937
peak=    3.474 closest distance to " O   HOH Z  44 " =    1.800
peak=    3.474 closest distance to " CA  ASN A 217 " =    1.202
peak=    3.468 closest distance to " CB  ASN A 215 " =    1.212
peak=    3.464 closest distance to " CA  ASP A 162 " =    0.998
peak=    3.464 closest distance to " O   HOH Z 389 " =    1.832
peak=    3.454 closest distance to " CB  SER A  26 " =    1.849
peak=    3.453 closest distance to " CB  GLN A  88 " =    1.202
peak=    3.447 closest distance to " CB  SER A   3 " =    1.252
peak=    3.447 closest distance to " CB  ALA A 291 " =    1.066
peak=    3.447 closest distance to " O   HOH Z 365 " =    2.822
peak=    3.440 closest distance to " CB  ALA A 114 " =    0.829
peak=    3.437 closest distance to " O   SER A 164 " =    1.391
peak=    3.434 closest distance to " O   HOH Z 213 " =    2.009
peak=    3.427 closest distance to " CG2 ILE A 239 " =    0.748
peak=    3.418 closest distance to " CB  SER A 212 " =    1.259
peak=    3.410 closest distance to " O   HOH Z 392 " =    2.822
peak=    3.403 closest distance to " O   HOH Z  97 " =    1.998
peak=    3.396 closest distance to " O   HOH Z 294 " =    1.548
peak=    3.393 closest distance to " O   HOH Z 280 " =    2.951
peak=    3.392 closest distance to " O   HOH Z 141 " =    1.684
peak=    3.385 closest distance to " O   HOH Z 325 " =    2.434
peak=    3.381 closest distance to " O   THR A 251 " =    1.078
peak=    3.380 closest distance to " O   ALA A 165 " =    1.560
peak=    3.378 closest distance to " O   HOH Z 250 " =    2.151
peak=    3.372 closest distance to " O   HOH Z  88 " =    2.648
peak=    3.371 closest distance to " N   PHE A 130 " =    1.183
peak=    3.367 closest distance to " OD1 ASN A  69 " =    2.615
peak=    3.364 closest distance to " NZ  LYS A  48 " =    1.139
peak=    3.361 closest distance to " CB  MET A  40 " =    0.817
peak=    3.359 closest distance to " CD2 LEU A 297 " =    0.941
peak=    3.357 closest distance to " O   HOH Z  59 " =    1.877
peak=    3.356 closest distance to " O   HOH Z 227 " =    1.441
peak=    3.354 closest distance to " CB  PRO A 198 " =    1.111
peak=    3.351 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.349 closest distance to " CA  MET A 105 " =    1.008
peak=    3.345 closest distance to " O   HOH Z   1 " =    2.083
peak=    3.341 closest distance to " CE1 TYR A 186 " =    1.387
peak=    3.335 closest distance to " O   HOH Z 171 " =    4.038
peak=    3.326 closest distance to " CB  ALA A 248 " =    1.364
peak=    3.322 closest distance to " O   HOH Z  62 " =    2.153
peak=    3.321 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.319 closest distance to " O   HOH Z  94 " =    2.308
peak=    3.318 closest distance to " CA  ALA A 100 " =    0.962
peak=    3.318 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.317 closest distance to " CG2 THR A 220 " =    0.793
peak=    3.317 closest distance to " CD  ARG A  66 " =    2.417
peak=    3.314 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.308 closest distance to " O   HOH Z  10 " =    1.777
peak=    3.307 closest distance to " CB  ASP A 191 " =    1.254
peak=    3.307 closest distance to " O   HOH Z 371 " =    1.631
peak=    3.305 closest distance to " O   HOH Z 371 " =    2.812
peak=    3.290 closest distance to " CH2 TRP A  70 " =    0.843
peak=    3.286 closest distance to " CD1 LEU A 261 " =    1.225
peak=    3.285 closest distance to " OE2 GLU A  53 " =    1.372
peak=    3.285 closest distance to " CB  MET A  47 " =    1.103
peak=    3.284 closest distance to " CB  ASN A 173 " =    1.057
peak=    3.276 closest distance to " O   HOH Z  28 " =    1.851
peak=    3.275 closest distance to " CG  GLN A  58 " =    1.002
peak=    3.272 closest distance to " CB  PRO A 243 " =    1.259
peak=    3.271 closest distance to " CB  SER A 273 " =    0.871
peak=    3.269 closest distance to " CG2 THR A  29 " =    1.211
peak=    3.266 closest distance to " O   HOH Z 273 " =    2.862
peak=    3.266 closest distance to " O   ALA A   1 " =    1.721
peak=    3.265 closest distance to " O   HOH Z 128 " =    2.153
peak=    3.265 closest distance to " O   HOH Z 290 " =    0.995
peak=    3.262 closest distance to " O   HOH Z 299 " =    4.428
peak=    3.247 closest distance to " O   HOH Z 421 " =    1.980
peak=    3.244 closest distance to " CA  ARG A 159 " =    1.297
peak=    3.243 closest distance to " CB  TYR A 116 " =    0.720
peak=    3.242 closest distance to " OG BSER A  99 " =    2.311
peak=    3.242 closest distance to " CA  THR A 221 " =    1.100
peak=    3.241 closest distance to " CA  ALA A 158 " =    1.340
peak=    3.240 closest distance to " O   HOH Z  97 " =    2.359
peak=    3.239 closest distance to " CB  ARG A 156 " =    1.079
peak=    3.237 closest distance to " CB  ARG A 156 " =    1.186
peak=    3.236 closest distance to " CB  SER A  62 " =    0.824
peak=    3.235 closest distance to " O   HOH Z 383 " =    1.945
peak=    3.232 closest distance to " CG  ARG A 138 " =    1.351
peak=    3.232 closest distance to " CA  ASP A 124 " =    0.777
peak=    3.231 closest distance to " O   HOH Z  88 " =    1.811
peak=    3.228 closest distance to " O   HOH Z  80 " =    1.729
peak=    3.225 closest distance to " CG1 ILE A 151 " =    1.003
peak=    3.220 closest distance to " OG1 THR A 264 " =    0.703
peak=    3.220 closest distance to " N   GLN A 278 " =    1.496
peak=    3.217 closest distance to " CG1 VAL A 153 " =    0.995
peak=    3.212 closest distance to " NH1 ARG A 138 " =    1.156
peak=    3.203 closest distance to " CA  ALA A 233 " =    1.428
peak=    3.202 closest distance to " O   GLY A  91 " =    1.430
peak=    3.201 closest distance to " O   HOH Z  80 " =    2.116
peak=    3.198 closest distance to " OD2 ASP A 286 " =    3.253
peak=    3.197 closest distance to " O   HOH Z 430 " =    5.327
peak=    3.184 closest distance to " CA  ARG A 102 " =    1.122
peak=    3.184 closest distance to " CA  LYS A 290 " =    1.144
peak=    3.177 closest distance to " CB  ARG A 138 " =    0.882
peak=    3.175 closest distance to " CB  GLU A  37 " =    0.999
peak=    3.168 closest distance to " N   VAL A 265 " =    1.426
peak=    3.168 closest distance to " CB  ARG A 139 " =    0.986
peak=    3.167 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.166 closest distance to " OG  SER A  62 " =    2.776
peak=    3.161 closest distance to " O   HOH Z 305 " =    3.620
peak=    3.160 closest distance to " O   HOH Z 234 " =    1.918
peak=    3.159 closest distance to " O   HOH Z 425 " =    1.309
peak=    3.156 closest distance to " CE3 TRP A 150 " =    1.134
peak=    3.153 closest distance to " O   HOH Z 106 " =    4.187
peak=    3.151 closest distance to " NE2 GLN A  77 " =    3.302
peak=    3.149 closest distance to " CG  LYS A  76 " =    0.944
peak=    3.140 closest distance to " O   HOH Z 245 " =    1.343
peak=    3.138 closest distance to " CB  ILE A 120 " =    1.295
peak=    3.130 closest distance to " CG2 THR A 221 " =    1.160
peak=    3.129 closest distance to " O   ASP A 191 " =    1.507
peak=    3.128 closest distance to " CA  ASP A 140 " =    1.200
peak=    3.127 closest distance to " CA  ALA A 248 " =    1.165
peak=    3.121 closest distance to " CB  PHE A 283 " =    0.707
peak=    3.121 closest distance to " O   HOH Z 198 " =    1.557
peak=    3.110 closest distance to " CA  ALA A  84 " =    1.246
peak=    3.108 closest distance to " O   HOH Z 233 " =    1.670
peak=    3.103 closest distance to " CA  ALA A 129 " =    1.404
peak=    3.098 closest distance to " N   ALA A 256 " =    1.132
peak=    3.094 closest distance to " NH2BARG A 145 " =    2.162
peak=    3.093 closest distance to " CB  GLN A 103 " =    0.788
peak=    3.091 closest distance to " CA  GLU A  46 " =    1.064
peak=    3.090 closest distance to " N   ASN A 127 " =    1.261
peak=    3.089 closest distance to " O   HOH Z 332 " =    1.533
peak=    3.082 closest distance to " O   HOH Z   1 " =    2.155
peak=    3.077 closest distance to " O   HOH Z 344 " =    3.122
peak=    3.073 closest distance to " CE2 PHE A  16 " =    0.932
peak=    3.058 closest distance to " CB  ALA A 227 " =    1.116
peak=    3.058 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.056 closest distance to " CB  ALA A 299 " =    0.998
peak=    3.051 closest distance to " N   ASP A 162 " =    1.187
peak=    3.044 closest distance to " O   HOH Z 120 " =    3.482
peak=    3.038 closest distance to " CA  ILE A 106 " =    0.798
peak=    3.036 closest distance to " OG BSER A  99 " =    2.797
peak=    3.001 closest distance to " CB  ARG A 102 " =    0.885

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.966 - 5.806
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 195
   mapped sites are within: 0.966 - 5.806

peak=   -4.982 closest distance to " CD  ARG A  14 " =    3.378
peak=   -4.490 closest distance to " C   HIS A 108 " =    1.084
peak=   -4.435 closest distance to " CD  GLN A  58 " =    1.008
peak=   -4.413 closest distance to " O   PRO A 198 " =    1.222
peak=   -4.270 closest distance to " CG1 VAL A 112 " =    2.616
peak=   -4.259 closest distance to " O   HOH Z 231 " =    2.292
peak=   -4.208 closest distance to " OG BSER A 134 " =    1.369
peak=   -4.196 closest distance to " CD  ARG A 156 " =    2.033
peak=   -4.192 closest distance to " CG1 VAL A 112 " =    2.831
peak=   -4.166 closest distance to " O   HOH Z 267 " =    5.591
peak=   -4.128 closest distance to " O   HOH Z 198 " =    1.458
peak=   -4.124 closest distance to " CG2 ILE A  49 " =    2.834
peak=   -4.123 closest distance to " CA  VAL A  67 " =    3.012
peak=   -4.118 closest distance to " O   HOH Z 377 " =    2.095
peak=   -4.101 closest distance to " O   VAL A  67 " =    2.630
peak=   -4.047 closest distance to " CD2 TYR A 293 " =    1.923
peak=   -3.991 closest distance to " CB  PRO A 243 " =    2.754
peak=   -3.956 closest distance to " O   HOH Z 290 " =    1.111
peak=   -3.924 closest distance to " CB  PHE A 192 " =    2.043
peak=   -3.921 closest distance to " CE2 PHE A  61 " =    2.648
peak=   -3.919 closest distance to " O   HOH Z 211 " =    1.293
peak=   -3.887 closest distance to " CG  GLN A 223 " =    2.108
peak=   -3.873 closest distance to " CA  ASP A 298 " =    1.113
peak=   -3.856 closest distance to " O   HOH Z 196 " =    2.029
peak=   -3.854 closest distance to " CE  MET A 105 " =    2.412
peak=   -3.841 closest distance to " CZ3 TRP A 179 " =    1.211
peak=   -3.835 closest distance to " CB  ALA A  43 " =    2.545
peak=   -3.829 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.810 closest distance to " O   ALA A  10 " =    1.708
peak=   -3.783 closest distance to " OXT GLY A 302 " =    2.915
peak=   -3.777 closest distance to " ND2 ASN A 249 " =    2.378
peak=   -3.777 closest distance to " CE BMET A  47 " =    1.338
peak=   -3.760 closest distance to " N   ALA A  43 " =    2.534
peak=   -3.738 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.699 closest distance to " CE2 TYR A  30 " =    2.680
peak=   -3.685 closest distance to " O   HOH Z 193 " =    1.226
peak=   -3.666 closest distance to " N   THR A  52 " =    1.699
peak=   -3.652 closest distance to " O   HOH Z 348 " =    2.247
peak=   -3.644 closest distance to " CB  GLN A  11 " =    1.765
peak=   -3.638 closest distance to " CG1 VAL A 250 " =    2.646
peak=   -3.635 closest distance to " CD1 LEU A 101 " =    2.386
peak=   -3.629 closest distance to " CB  ASN A  39 " =    2.278
peak=   -3.626 closest distance to " O   HOH Z  73 " =    2.392
peak=   -3.609 closest distance to " CG  ARG A 269 " =    2.297
peak=   -3.608 closest distance to " CG  PRO A 198 " =    1.832
peak=   -3.600 closest distance to " O   HOH Z 102 " =    1.521
peak=   -3.596 closest distance to " O   HOH Z 174 " =    2.652
peak=   -3.595 closest distance to " CG  GLU A 277 " =    1.250
peak=   -3.595 closest distance to " CB  ALA A 161 " =    2.576
peak=   -3.591 closest distance to " O   HOH Z 372 " =    2.293
peak=   -3.586 closest distance to " OD2 ASP A 191 " =    1.392
peak=   -3.574 closest distance to " O   SER A 210 " =    1.995
peak=   -3.571 closest distance to " O   HOH Z 185 " =    2.365
peak=   -3.563 closest distance to " CE3 TRP A 150 " =    2.342
peak=   -3.556 closest distance to " OD1 ASN A 148 " =    1.391
peak=   -3.547 closest distance to " O   HOH Z 162 " =    3.398
peak=   -3.534 closest distance to " O   HOH Z 407 " =    2.926
peak=   -3.524 closest distance to " O   HOH Z 216 " =    1.176
peak=   -3.523 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.514 closest distance to " O   HOH Z  38 " =    1.647
peak=   -3.509 closest distance to " OE1 GLN A  88 " =    1.081
peak=   -3.494 closest distance to " CD  PRO A 243 " =    2.108
peak=   -3.493 closest distance to " O   TRP A  70 " =    1.473
peak=   -3.493 closest distance to " CZ  PHE A 155 " =    1.120
peak=   -3.490 closest distance to " O   HOH Z   6 " =    2.337
peak=   -3.490 closest distance to " CB  HIS A  86 " =    1.130
peak=   -3.489 closest distance to " ND2 ASN A  45 " =    1.136
peak=   -3.487 closest distance to " CG1BVAL A  41 " =    2.794
peak=   -3.486 closest distance to " CG  MET A 105 " =    1.031
peak=   -3.467 closest distance to " ND2 ASN A  45 " =    1.831
peak=   -3.464 closest distance to " CB  ALA A 248 " =    2.323
peak=   -3.462 closest distance to " CA  GLY A 241 " =    2.384
peak=   -3.461 closest distance to " O   HOH Z 429 " =    1.967
peak=   -3.459 closest distance to " N   ALA A 248 " =    1.642
peak=   -3.454 closest distance to " O   VAL A 174 " =    2.212
peak=   -3.443 closest distance to " CD  ARG A  79 " =    1.178
peak=   -3.436 closest distance to " O   PRO A 163 " =    1.949
peak=   -3.435 closest distance to " CZ3 TRP A 274 " =    2.389
peak=   -3.432 closest distance to " O   VAL A 189 " =    2.634
peak=   -3.426 closest distance to " CB  ALA A 291 " =    2.041
peak=   -3.424 closest distance to " CD1 ILE A 239 " =    2.354
peak=   -3.418 closest distance to " O   PHE A 218 " =    1.500
peak=   -3.416 closest distance to " O   HOH Z 166 " =    1.944
peak=   -3.414 closest distance to " O   HOH Z 326 " =    5.072
peak=   -3.413 closest distance to " CA  GLY A 203 " =    2.373
peak=   -3.409 closest distance to " OD1 ASP A 171 " =    1.590
peak=   -3.409 closest distance to " O   ALA A 292 " =    2.132
peak=   -3.405 closest distance to " CG  LEU A  83 " =    2.012
peak=   -3.402 closest distance to " CB  ALA A  10 " =    2.300
peak=   -3.395 closest distance to " O   HOH Z 295 " =    1.606
peak=   -3.394 closest distance to " O   HOH Z  60 " =    1.934
peak=   -3.392 closest distance to " CG2 ILE A 263 " =    2.297
peak=   -3.384 closest distance to " CG1 VAL A 125 " =    1.899
peak=   -3.384 closest distance to " O   ASN A 252 " =    1.350
peak=   -3.381 closest distance to " NH2AARG A 275 " =    5.261
peak=   -3.373 closest distance to " CD1 LEU A 255 " =    2.818
peak=   -3.373 closest distance to " O   HOH Z  71 " =    2.598
peak=   -3.370 closest distance to " CG1 VAL A 265 " =    2.834
peak=   -3.369 closest distance to " CA  ILE A 263 " =    1.045
peak=   -3.368 closest distance to " O   HOH Z  10 " =    1.456
peak=   -3.365 closest distance to " CD1 ILE A 199 " =    2.462
peak=   -3.361 closest distance to " O   HOH Z 359 " =    3.015
peak=   -3.355 closest distance to " NH2 ARG A  79 " =    1.530
peak=   -3.354 closest distance to " O   HOH Z 131 " =    4.074
peak=   -3.351 closest distance to " O   HOH Z  64 " =    1.535
peak=   -3.348 closest distance to " O   HOH Z  37 " =    1.790
peak=   -3.345 closest distance to " O   ARG A  24 " =    1.708
peak=   -3.336 closest distance to " CZ  ARG A 259 " =    0.966
peak=   -3.329 closest distance to " CB  ASP A 132 " =    2.293
peak=   -3.322 closest distance to " NE2 GLN A 278 " =    1.588
peak=   -3.318 closest distance to " CD  GLU A 236 " =    1.103
peak=   -3.314 closest distance to " C   LEU A 143 " =    1.023
peak=   -3.311 closest distance to " O   HOH Z 174 " =    3.753
peak=   -3.308 closest distance to " O   HOH Z 278 " =    1.332
peak=   -3.308 closest distance to " O   SER A  95 " =    1.638
peak=   -3.305 closest distance to " CG  ARG A  66 " =    2.404
peak=   -3.298 closest distance to " O   ILE A 106 " =    1.885
peak=   -3.297 closest distance to " O   HOH Z  63 " =    1.709
peak=   -3.297 closest distance to " CG  PHE A 283 " =    2.629
peak=   -3.296 closest distance to " ND2 ASN A 187 " =    1.597
peak=   -3.294 closest distance to " O   VAL A 189 " =    1.739
peak=   -3.293 closest distance to " CB  ALA A 129 " =    2.452
peak=   -3.290 closest distance to " O   HOH Z 285 " =    1.757
peak=   -3.289 closest distance to " O   HOH Z 374 " =    1.928
peak=   -3.284 closest distance to " ND2 ASN A  60 " =    1.300
peak=   -3.283 closest distance to " O   HOH Z 313 " =    1.868
peak=   -3.280 closest distance to " O   HOH Z 171 " =    1.937
peak=   -3.279 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.277 closest distance to " O   HOH Z 357 " =    2.106
peak=   -3.276 closest distance to " O   HOH Z 252 " =    3.998
peak=   -3.274 closest distance to " O   HOH Z 149 " =    2.204
peak=   -3.274 closest distance to " O   ALA A 180 " =    1.013
peak=   -3.268 closest distance to " O   ALA A  34 " =    2.313
peak=   -3.266 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.261 closest distance to " CB  TRP A  85 " =    2.544
peak=   -3.252 closest distance to " O   HOH Z 114 " =    3.099
peak=   -3.247 closest distance to " OH  TYR A 172 " =    1.912
peak=   -3.246 closest distance to " O   HOH Z 275 " =    1.482
peak=   -3.244 closest distance to " O   ALA A 180 " =    1.273
peak=   -3.230 closest distance to " O   HOH Z   6 " =    1.426
peak=   -3.229 closest distance to " O   TYR A 247 " =    2.847
peak=   -3.224 closest distance to " CG  TRP A 266 " =    1.961
peak=   -3.216 closest distance to " O   HOH Z 154 " =    2.132
peak=   -3.215 closest distance to " O   HOH Z 165 " =    2.040
peak=   -3.214 closest distance to " O   HOH Z 318 " =    1.947
peak=   -3.214 closest distance to " CB  ASP A 286 " =    2.108
peak=   -3.213 closest distance to " O   HOH Z 298 " =    2.540
peak=   -3.212 closest distance to " O   HOH Z 191 " =    5.806
peak=   -3.206 closest distance to " O   HOH Z 351 " =    1.647
peak=   -3.206 closest distance to " O   HOH Z 232 " =    1.668
peak=   -3.201 closest distance to " OD1 ASN A 301 " =    1.847
peak=   -3.195 closest distance to " OD2 ASP A  50 " =    2.082
peak=   -3.186 closest distance to " CD2 HIS A 207 " =    2.256
peak=   -3.185 closest distance to " O   HOH Z 128 " =    2.605
peak=   -3.185 closest distance to " O   SER A 135 " =    1.484
peak=   -3.181 closest distance to " CB  PHE A  16 " =    2.494
peak=   -3.176 closest distance to " CG2 THR A 178 " =    2.419
peak=   -3.175 closest distance to " O   HOH Z 265 " =    2.451
peak=   -3.174 closest distance to " CD2 PHE A  61 " =    2.322
peak=   -3.170 closest distance to " O   HOH Z 281 " =    2.706
peak=   -3.167 closest distance to " O   HOH Z 283 " =    5.462
peak=   -3.160 closest distance to " O   HOH Z 389 " =    1.990
peak=   -3.160 closest distance to " C   GLY A 262 " =    1.977
peak=   -3.159 closest distance to " O   GLU A 152 " =    1.334
peak=   -3.157 closest distance to " CD  ARG A 139 " =    1.697
peak=   -3.156 closest distance to " C   MET A 188 " =    1.356
peak=   -3.155 closest distance to " O   HOH Z  52 " =    1.615
peak=   -3.148 closest distance to " OH  TYR A 247 " =    2.123
peak=   -3.141 closest distance to " CA  ASP A  27 " =    2.450
peak=   -3.139 closest distance to " N   ASP A 286 " =    2.280
peak=   -3.135 closest distance to " C   SER A 206 " =    1.500
peak=   -3.135 closest distance to " O   TYR A 186 " =    1.651
peak=   -3.133 closest distance to " O   HOH Z 110 " =    1.385
peak=   -3.133 closest distance to " OE1 GLN A 183 " =    1.698
peak=   -3.128 closest distance to " CA  GLY A  57 " =    2.097
peak=   -3.125 closest distance to " CB  ALA A 100 " =    2.248
peak=   -3.122 closest distance to " OG BSER A 134 " =    1.922
peak=   -3.120 closest distance to " O   HOH Z   9 " =    1.775
peak=   -3.116 closest distance to " CG1AVAL A  41 " =    2.651
peak=   -3.113 closest distance to " O   HOH Z 389 " =    1.473
peak=   -3.106 closest distance to " OD2 ASP A 171 " =    2.432
peak=   -3.102 closest distance to " CD1 LEU A   5 " =    2.445
peak=   -3.095 closest distance to " O   ARG A 145 " =    1.639
peak=   -3.091 closest distance to " CG2 VAL A 189 " =    2.142
peak=   -3.089 closest distance to " CD1 TRP A  70 " =    1.091
peak=   -3.087 closest distance to " O   HOH Z 156 " =    3.516
peak=   -3.087 closest distance to " CG  GLU A  53 " =    1.559
peak=   -3.085 closest distance to " O   HOH Z 200 " =    4.578
peak=   -3.085 closest distance to " O   HOH Z 219 " =    4.449
peak=   -3.081 closest distance to " NZ  LYS A 166 " =    1.333
peak=   -3.072 closest distance to " O   TRP A  70 " =    2.034
peak=   -3.070 closest distance to " O   TRP A  92 " =    2.013
peak=   -3.035 closest distance to " O   HOH Z 139 " =    4.877
peak=   -3.029 closest distance to " CA  GLY A  23 " =    2.618
peak=   -3.027 closest distance to " O   GLY A  80 " =    2.503

================= 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    :  0.3816 0.3757   6.172367e+00   6.152457e+00
   1_bss:  0.3647 0.3593   6.147714e+00   6.125090e+00
   1_xyz:  0.2378 0.2629   5.761039e+00   5.841319e+00
   1_adp:  0.2160 0.2722   5.709130e+00   5.872871e+00
   1_occ:  0.2157 0.2724   5.709206e+00   5.874319e+00
   2_bss:  0.2105 0.2692   5.694964e+00   5.867614e+00
   2_xyz:  0.1495 0.1988   5.392666e+00   5.603990e+00
   2_adp:  0.1381 0.1833   5.316170e+00   5.524598e+00
   2_occ:  0.1379 0.1831   5.315139e+00   5.523785e+00
   3_bss:  0.1376 0.1816   5.310585e+00   5.518587e+00
   3_xyz:  0.1193 0.1642   5.195526e+00   5.424853e+00
   3_adp:  0.1156 0.1628   5.177018e+00   5.416601e+00
   3_occ:  0.1155 0.1629   5.177164e+00   5.416885e+00
   4_bss:  0.1154 0.1629   5.176821e+00   5.416851e+00
   4_xyz:  0.1148 0.1611   5.172119e+00   5.411800e+00
   4_adp:  0.1149 0.1596   5.170266e+00   5.406514e+00
   4_occ:  0.1148 0.1596   5.170251e+00   5.406845e+00
   5_bss:  0.1148 0.1586   5.168367e+00   5.402801e+00
   5_xyz:  0.1156 0.1596   5.175848e+00   5.409236e+00
   5_adp:  0.1150 0.1605   5.176036e+00   5.414508e+00
   5_occ:  0.1150 0.1604   5.176090e+00   5.414699e+00
   5_bss:  0.1149 0.1603   5.176201e+00   5.414809e+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:  0.311  41.613  -2.365  -3.030   6.070  -0.000   0.000   0.000
   1_xyz:  0.311  41.613  -2.365  -3.030   6.070  -0.000   0.000   0.000
   1_adp:  0.311  41.613  -2.365  -3.030   6.070  -0.000   0.000   0.000
   1_occ:  0.311  41.613  -2.365  -3.030   6.070  -0.000   0.000   0.000
   2_bss:  0.311  58.074  -2.924  -2.626   1.295  -0.000   0.000   0.000
   2_xyz:  0.311  58.074  -2.924  -2.626   1.295  -0.000   0.000   0.000
   2_adp:  0.311  58.074  -2.924  -2.626   1.295  -0.000   0.000   0.000
   2_occ:  0.311  58.074  -2.924  -2.626   1.295  -0.000   0.000   0.000
   3_bss:  0.330  63.161  -3.018  -2.427   0.091  -0.000   0.000   0.000
   3_xyz:  0.330  63.161  -3.018  -2.427   0.091  -0.000   0.000   0.000
   3_adp:  0.330  63.161  -3.018  -2.427   0.091  -0.000   0.000   0.000
   3_occ:  0.330  63.161  -3.018  -2.427   0.091  -0.000   0.000   0.000
   4_bss:  0.330  63.161  -2.794  -2.210  -0.119  -0.000  -0.000  -0.000
   4_xyz:  0.330  63.161  -2.794  -2.210  -0.119  -0.000  -0.000  -0.000
   4_adp:  0.330  63.161  -2.794  -2.210  -0.119  -0.000  -0.000  -0.000
   4_occ:  0.330  63.161  -2.794  -2.210  -0.119  -0.000  -0.000  -0.000
   5_bss:  0.330  63.161  -2.734  -2.119  -0.176  -0.000  -0.000  -0.000
   5_xyz:  0.330  63.161  -2.734  -2.119  -0.176  -0.000  -0.000  -0.000
   5_adp:  0.330  63.161  -2.734  -2.119  -0.176  -0.000  -0.000  -0.000
   5_occ:  0.330  63.161  -2.734  -2.119  -0.176  -0.000  -0.000  -0.000
   5_bss:  0.330  63.135  -2.525  -1.918  -0.027  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.915 0.6343  0.8026    41951.103
   1_bss:  39.387 0.6511  0.8317    38234.708
   1_xyz:  26.052 0.8013  0.9808    17797.068
   1_adp:  27.311 0.7870  0.9736    19139.731
   1_occ:  27.377 0.7863  0.9725    19204.744
   2_bss:  26.684 0.7940  0.9290    18673.059
   2_xyz:  19.165 0.8691  0.9762    10039.421
   2_adp:  17.255 0.8871  0.9759     8689.692
   2_occ:  17.233 0.8873  0.9761     8670.788
   3_bss:  17.074 0.8887  0.9649     8544.428
   3_xyz:  14.933 0.9070  0.9755     6966.612
   3_adp:  14.692 0.9094  0.9694     6834.503
   3_occ:  14.699 0.9093  0.9693     6835.651
   4_bss:  14.691 0.9094  0.9722     6835.362
   4_xyz:  14.484 0.9112  0.9729     6722.626
   4_adp:  14.375 0.9123  0.9675     6677.334
   4_occ:  14.382 0.9122  0.9674     6679.009
   5_bss:  14.327 0.9126  0.9686     6599.743
   5_xyz:  14.395 0.9122  0.9686     6656.931
   5_adp:  14.499 0.9113  0.9618     6703.481
   5_occ:  14.500 0.9113  0.9617     6704.238
   5_bss:  14.503 0.9113  0.9672     6705.924
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7937e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7937e-01
   1_xyz:   1.332  0.011  0.087 15.488  0.006  4.108   9.9890e-02
   1_adp:   1.332  0.011  0.087 15.488  0.006  4.108   9.9890e-02
   1_occ:   1.332  0.011  0.087 15.488  0.006  4.108   9.9890e-02
   2_bss:   1.332  0.011  0.087 15.488  0.006  4.108   9.9890e-02
   2_xyz:   1.096  0.008  0.078 15.025  0.004  4.130   6.8274e-02
   2_adp:   1.096  0.008  0.078 15.025  0.004  4.130   6.8274e-02
   2_occ:   1.096  0.008  0.078 15.025  0.004  4.130   6.8274e-02
   3_bss:   1.096  0.008  0.078 15.025  0.004  4.130   6.8274e-02
   3_xyz:   1.113  0.011  0.083 14.992  0.005  4.140   7.4396e-02
   3_adp:   1.113  0.011  0.083 14.992  0.005  4.140   7.4396e-02
   3_occ:   1.113  0.011  0.083 14.992  0.005  4.140   7.4396e-02
   4_bss:   1.113  0.011  0.083 14.992  0.005  4.140   7.4396e-02
   4_xyz:   1.008  0.008  0.077 14.628  0.004  4.124   6.1190e-02
   4_adp:   1.008  0.008  0.077 14.628  0.004  4.124   6.1190e-02
   4_occ:   1.008  0.008  0.077 14.628  0.004  4.124   6.1190e-02
   5_bss:   1.008  0.008  0.077 14.628  0.004  4.124   6.1190e-02
   5_xyz:   0.938  0.007  0.072 14.376  0.003  4.125   5.2767e-02
   5_adp:   0.938  0.007  0.072 14.376  0.003  4.125   5.2767e-02
   5_occ:   0.938  0.007  0.072 14.376  0.003  4.125   5.2767e-02
   5_bss:   0.938  0.007  0.072 14.376  0.003  4.125   5.2767e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.324   2.4305e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.324   2.4305e-01
   1_xyz:  10.321  0.058  0.417 82.905  0.049  2.097   1.0780e-01
   1_adp:  10.321  0.058  0.417 82.905  0.049  2.097   1.0780e-01
   1_occ:  10.321  0.058  0.417 82.905  0.049  2.097   1.0780e-01
   2_bss:  10.321  0.058  0.417 82.905  0.049  2.097   1.0780e-01
   2_xyz:   7.171  0.040  0.248 85.040  0.045  2.220   5.3319e-02
   2_adp:   7.171  0.040  0.248 85.040  0.045  2.220   5.3319e-02
   2_occ:   7.171  0.040  0.248 85.040  0.045  2.220   5.3319e-02
   3_bss:   7.171  0.040  0.248 85.040  0.045  2.220   5.3319e-02
   3_xyz:   7.316  0.067  0.275 83.922  0.039  2.331   5.9637e-02
   3_adp:   7.316  0.067  0.275 83.922  0.039  2.331   5.9637e-02
   3_occ:   7.316  0.067  0.275 83.922  0.039  2.331   5.9637e-02
   4_bss:   7.316  0.067  0.275 83.922  0.039  2.331   5.9637e-02
   4_xyz:   6.669  0.049  0.246 83.013  0.036  2.388   4.2955e-02
   4_adp:   6.669  0.049  0.246 83.013  0.036  2.388   4.2955e-02
   4_occ:   6.669  0.049  0.246 83.013  0.036  2.388   4.2955e-02
   5_bss:   6.669  0.049  0.246 83.013  0.036  2.388   4.2955e-02
   5_xyz:   6.463  0.045  0.218 83.240  0.032  2.413   2.9921e-02
   5_adp:   6.463  0.045  0.218 83.240  0.032  2.413   2.9921e-02
   5_occ:   6.463  0.045  0.218 83.240  0.032  2.413   2.9921e-02
   5_bss:   6.463  0.045  0.218 83.240  0.032  2.413   2.9921e-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:  78.64   0.00  17.70  70.84   0.00  13.52  78.64   3.89  40.51
   1_occ:  78.64   0.00  17.70  70.84   0.00  13.52  78.64   3.89  40.51
   2_bss:  78.64   0.00  17.70  70.84   0.00  13.52  78.64   3.89  40.51
   2_xyz:  78.64   0.00  17.70  70.84   0.00  13.52  78.64   3.89  40.51
   2_adp:  77.26   1.07  17.13  71.87   1.07  12.94  77.26   5.95  39.98
   2_occ:  77.26   1.07  17.13  71.87   1.07  12.94  77.26   5.95  39.98
   3_bss:  77.26   1.07  17.13  71.87   1.07  12.94  77.26   5.95  39.98
   3_xyz:  77.26   1.07  17.13  71.87   1.07  12.94  77.26   5.95  39.98
   3_adp:  87.68   1.02  17.29  82.15   1.02  12.91  87.68   5.40  41.16
   3_occ:  87.68   1.02  17.29  82.15   1.02  12.91  87.68   5.40  41.16
   4_bss:  87.68   1.02  17.29  82.15   1.02  12.91  87.68   5.40  41.16
   4_xyz:  87.68   1.02  17.29  82.15   1.02  12.91  87.68   5.40  41.16
   4_adp:  86.61   1.50  16.82  81.89   1.50  12.68  86.61   1.70  39.35
   4_occ:  86.61   1.50  16.82  81.89   1.50  12.68  86.61   1.70  39.35
   5_bss:  86.61   1.50  16.82  81.89   1.50  12.68  86.61   1.70  39.35
   5_xyz:  86.61   1.50  16.82  81.89   1.50  12.68  86.61   1.70  39.35
   5_adp:  89.67   0.77  16.79  84.47   0.77  12.58  89.67   2.97  39.71
   5_occ:  89.67   0.77  16.79  84.47   0.77  12.58  89.67   2.97  39.71
   5_bss:  89.64   0.74  16.76  84.45   0.74  12.55  89.64   2.95  39.68
------------------------------------------------------------------------
 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:    1.977    0.022    0.402
   1_adp:    1.977    0.022    0.402
   1_occ:    1.977    0.022    0.402
   2_bss:    1.977    0.022    0.402
   2_xyz:    1.590    0.035    0.470
   2_adp:    1.590    0.035    0.470
   2_occ:    1.590    0.035    0.470
   3_bss:    1.590    0.035    0.470
   3_xyz:    1.139    0.030    0.510
   3_adp:    1.139    0.030    0.510
   3_occ:    1.139    0.030    0.510
   4_bss:    1.139    0.030    0.510
   4_xyz:    1.280    0.026    0.519
   4_adp:    1.280    0.026    0.519
   4_occ:    1.280    0.026    0.519
   5_bss:    1.280    0.026    0.519
   5_xyz:    1.580    0.032    0.528
   5_adp:    1.580    0.032    0.528
   5_occ:    1.580    0.032    0.528
   5_bss:    1.580    0.032    0.528
------------------------------------------------------------------------

CPU time actual refinement: 324.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/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_428/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_428/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.75 
  Macro-tasks:
    bulk solvent and scale       = 37.42  
    individual site refinement   = 135.70 
    weights calculation          = 29.73  
    collect and process          = 6.64   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 209.59 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 102.08 
    alpha_beta                      = 8.45   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 112.32 
    fmodel                         = 6.46   
    r_factors                      = 0.15   
    phase_errors                   = 11.02  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 243.67 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.569 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    648 calls, 101.71 s
gradients_fft:          593 calls,  98.43 s

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

# Date 2008-01-16 Time 04:48:38 PST -0800 (1200487718.95 s)
Start R-work = 0.3816, R-free = 0.3757 (no bulk solvent and anisotropic scale)
Final R-work = 0.1374, R-free = 0.1787 (no bulk solvent and anisotropic scale)

Start R-work = 0.3647, R-free = 0.3593
Final R-work = 0.1149, R-free = 0.1603