# Date 2008-01-16 Time 04:09:07 PST -0800 (1200485347.08 s)
#phil __OFF__

Command line arguments: "../196.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9212
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 196

-------------------------------------------------------------------------------
  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: (68.845, 47.1647, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8854 1.96091
Completeness in resolution range: 0.926544
Completeness with d_max=infinity: 0.923748

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8854
                             d_min =   1.9609

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: (68.845, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8854 1.96091
Completeness in resolution range: 0.926544
Completeness with d_max=infinity: 0.923748

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8858 -  4.1961 [2221/2249]  1996   225  10.1%
  bin  2:  4.1961 -  3.3429 [2128/2151]  1912   216  10.2%
  bin  3:  3.3429 -  2.9240 [2110/2132]  1908   202   9.6%
  bin  4:  2.9240 -  2.6583 [2089/2108]  1873   216  10.3%
  bin  5:  2.6583 -  2.4687 [2065/2094]  1853   212  10.3%
  bin  6:  2.4687 -  2.3237 [2051/2093]  1853   198   9.7%
  bin  7:  2.3237 -  2.2077 [2048/2084]  1846   202   9.9%
  bin  8:  2.2077 -  2.1119 [2060/2101]  1852   208  10.1%
  bin  9:  2.1119 -  2.0308 [2021/2064]  1828   193   9.5%
  bin 10:  2.0308 -  1.9609 [ 796/2066]   709    87  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/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:
        1.27 -     2.00: 11
        2.00 -     2.72: 196
        2.72 -     3.45: 4603
        3.45 -     4.17: 9363
        4.17 -     4.90: 14148
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.273 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.421 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.443 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.485 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.659 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28316 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_196/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 68.845 47.16465 88.1178 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: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4090   r_free= 0.4069   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.203098                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8858 -  4.6802 0.99   1443  159 0.3128 0.3241      6.4443       6.446|
|  2:  4.6802 -  3.7341 0.99   1396  154 0.3279 0.3318      6.6286       6.667|
|  3:  3.7341 -  3.2678 0.99   1357  156 0.3815 0.3563      6.5595       6.544|
|  4:  3.2678 -  2.9716 0.99   1351  140 0.3976 0.4303      6.4044      6.4677|
|  5:  2.9716 -  2.7600 0.99   1339  154 0.4270 0.4000      6.2681      6.2697|
|  6:  2.7600 -  2.5982 0.98   1331  148 0.4393 0.4773      6.2006      6.1263|
|  7:  2.5982 -  2.4687 0.99   1325  160 0.4365 0.3707      6.1484      6.0488|
|  8:  2.4687 -  2.3617 0.99   1344  138 0.4649 0.4553       6.116      6.0945|
|  9:  2.3617 -  2.2711 0.98   1329  144 0.4693 0.4476      6.0718      6.1234|
| 10:  2.2711 -  2.1930 0.98   1306  143 0.4729 0.4833      6.0499      6.0183|
| 11:  2.1930 -  2.1246 0.98   1301  159 0.4753 0.4808      5.9676      5.9728|
| 12:  2.1246 -  2.0640 0.99   1339  141 0.4739 0.4720       5.914       5.931|
| 13:  2.0640 -  2.0098 0.86   1157  118 0.4765 0.4995      5.8415      5.8303|
| 14:  2.0098 -  1.9609 0.24    312   45 0.4622 0.4314      5.8657      5.6836|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8858 -  4.6802  1443   159  0.76  29.12   0.85     0.77      52377.92|
|  2:  4.6802 -  3.7341  1396   154  0.77  28.66   0.95     0.86      74118.47|
|  3:  3.7341 -  3.2678  1357   156  0.69  35.92   0.94     0.86      78564.12|
|  4:  3.2678 -  2.9716  1351   140  0.62  42.46   0.94     0.79      71518.73|
|  5:  2.9716 -  2.7600  1339   154  0.56  47.37   0.94     0.74      57863.54|
|  6:  2.7600 -  2.5982  1331   148  0.55  48.15   0.93     0.73      49811.25|
|  7:  2.5982 -  2.4687  1325   160  0.57  46.54   0.94     0.76      43143.19|
|  8:  2.4687 -  2.3617  1344   138  0.56  47.53   0.95     0.77      38596.36|
|  9:  2.3617 -  2.2711  1329   144  0.56  47.33   0.95     0.79      36265.65|
| 10:  2.2711 -  2.1930  1306   143  0.54  49.26   0.96     0.73      34102.35|
| 11:  2.1930 -  2.1246  1301   159  0.49  53.05   0.95     0.73      36353.25|
| 12:  2.1246 -  2.0640  1339   141  0.44  57.20   0.99     0.68      35455.97|
| 13:  2.0640 -  2.0098  1157   118  0.42  58.61   0.95     0.66      32534.98|
| 14:  2.0098 -  1.9609   312    45  0.47  54.25   1.02     0.62      25231.37|
|alpha:            min =        0.62 max =            0.86 mean =         0.76|
|beta:             min =    25231.37 max =        78564.12 mean =     49241.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.31|
|phase err.(test): min =        0.00 max =           89.97 mean =        45.34|
|-----------------------------------------------------------------------------|

============================== 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 = 5.269009              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.076   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.155891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.624   (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 |  1.273 -  1.636:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.636 -  1.998:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.998 -  2.361:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.361 -  2.724:      173 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.724 -  3.086:     2322 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.086 -  3.449:     2281 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.449 -  3.812:     4133 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.812 -  4.175:     5230 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.175 -  4.537:     6357 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.537 -  4.900:     7791 |
|-----------------------------------------------------------------------------|
|-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 |        0.195 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.273 |       0.652 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    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: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4090   r_free= 0.4069   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.203098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3989   r_free= 0.3962   ksol= 0.32   Bsol= 36.87   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-2.22,3.67,-0.00,0.00,0.00); trace/3= 0.31                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.189660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.579876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.682   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.225   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3989      final r-factor (work) = 0.2809          |
| start r-factor (free) = 0.3962      final r-factor (free) = 0.3058          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3714 = 4.58 * 0.50 * 6.1908 + 1.00 * 0.1947                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8487 = 4.58 * 0.50 * 6.0073 + 1.00 * 0.0924                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2809      final r-factor (work) = 0.2588          |
| start r-factor (free) = 0.3058      final r-factor (free) = 0.3102          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0968 = 0.68 * 1.00 * 6.0073 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0430 = 0.68 * 1.00 * 5.8525 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.44   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    98.44   16.97    None  None   None       |
|    Sol.    : 438    0      4.34    65.08   37.57    None  None   None       |
|    Mac.    : 2385   0      0.00    98.44   13.19    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:     0.000 -   9.844:  890   |   5:    49.222 -  59.066:   85        |
|      1:     9.844 -  19.689: 1142   |   6:    59.066 -  68.910:    5        |
|      2:    19.689 -  29.533:  386   |   7:    68.910 -  78.755:    0        |
|      3:    29.533 -  39.377:  156   |   8:    78.755 -  88.599:    0        |
|      4:    39.377 -  49.222:  158   |   9:    88.599 -  98.443:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2588 r_free = 0.3102             target_work(ml) = 5.858         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2584 r_free = 0.3102             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2584   r_free= 0.3102   ksol= 0.32   Bsol= 36.87   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-2.22,3.67,-0.00,0.00,0.00); trace/3= 0.31                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.857354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.3077   ksol= 0.33   Bsol= 52.47   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.02,1.19,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.852606                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.664131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.560087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.404   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2559      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.3077      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6716 = 5.66 * 0.50 * 5.8541 + 1.00 * 0.0924                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2216 = 5.66 * 0.50 * 5.7025 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1502          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.2024          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2832 = 0.56 * 1.00 * 5.7025 + 1.00 * 0.0893                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0524 = 0.56 * 1.00 * 5.4315 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.92   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    76.92   17.55    None  None   None       |
|    Sol.    : 438    0      5.47    75.74   41.45    None  None   None       |
|    Mac.    : 2385   0      0.00    76.92   13.16    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 -   7.692:  536   |   5:    38.460 -  46.152:   99        |
|      1:     7.692 -  15.384: 1288   |   6:    46.152 -  53.844:   95        |
|      2:    15.384 -  23.076:  417   |   7:    53.844 -  61.535:   82        |
|      3:    23.076 -  30.768:  152   |   8:    61.535 -  69.227:   35        |
|      4:    30.768 -  38.460:  102   |   9:    69.227 -  76.919:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1502 r_free = 0.2024             target_work(ml) = 5.397         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1501 r_free = 0.2024             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1501   r_free= 0.2024   ksol= 0.33   Bsol= 52.47   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.02,1.19,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.396046                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1500   r_free= 0.2013   ksol= 0.32   Bsol= 59.69   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.01,0.03,-0.00,0.00,0.00); trace/3= -1.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.392708                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.384624              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.906   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.469557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.799  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1500      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.2013      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5508 = 2.38 * 0.50 * 5.4342 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4142 = 2.38 * 0.50 * 5.3323 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5141 = 0.47 * 1.00 * 5.3323 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4704 = 0.47 * 1.00 * 5.2401 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    84.20   17.38    None  None   None       |
|    all(noH): 2823   0      0.76    84.20   17.38    None  None   None       |
|    Sol.    : 438    0      5.11    83.00   41.42    None  None   None       |
|    Mac.    : 2385   0      0.76    84.20   12.96    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:     0.758 -   9.102:  850   |   5:    42.478 -  50.822:   98        |
|      1:     9.102 -  17.446: 1194   |   6:    50.822 -  59.166:   86        |
|      2:    17.446 -  25.790:  279   |   7:    59.166 -  67.510:   49        |
|      3:    25.790 -  34.134:  130   |   8:    67.510 -  75.854:   22        |
|      4:    34.134 -  42.478:  105   |   9:    75.854 -  84.197:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1696             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1696             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1696   ksol= 0.32   Bsol= 59.69   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.01,0.03,-0.00,0.00,0.00); trace/3= -1.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.232849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1695   ksol= 0.33   Bsol= 59.69   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-2.00,-0.33,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.232399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.900118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.997  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.779  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0348 = 1.90 * 0.50 * 5.2401 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0072 = 1.90 * 0.50 * 5.2106 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2210 = 0.62 * 1.00 * 5.2106 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2050 = 0.62 * 1.00 * 5.1844 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.11   17.17    None  None   None       |
|    all(noH): 2823   0      0.00    90.11   17.17    None  None   None       |
|    Sol.    : 438    0      0.00    90.11   41.10    None  None   None       |
|    Mac.    : 2385   0      0.70    88.49   12.78    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 -   9.011:  853   |   5:    45.054 -  54.065:   90        |
|      1:     9.011 -  18.022: 1242   |   6:    54.065 -  63.075:   75        |
|      2:    18.022 -  27.032:  259   |   7:    63.075 -  72.086:   32        |
|      3:    27.032 -  36.043:  124   |   8:    72.086 -  81.097:   18        |
|      4:    36.043 -  45.054:  124   |   9:    81.097 -  90.108:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1622             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1622             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1622   ksol= 0.33   Bsol= 59.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-2.00,-0.33,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183665                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1619   ksol= 0.33   Bsol= 59.69   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-1.84,-0.27,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183025                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.866199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.556  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.405476              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.148  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8946 = 1.87 * 0.50 * 5.1847 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8848 = 1.87 * 0.50 * 5.1737 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1078 = 0.41 * 1.00 * 5.1737 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1060 = 0.41 * 1.00 * 5.1705 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.37   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    90.37   16.84    None  None   None       |
|    Sol.    : 438    0      0.00    90.37   40.18    None  None   None       |
|    Mac.    : 2385   0      0.76    89.49   12.56    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 -   9.037:  894   |   5:    45.186 -  54.223:   94        |
|      1:     9.037 -  18.075: 1227   |   6:    54.223 -  63.261:   62        |
|      2:    18.075 -  27.112:  245   |   7:    63.261 -  72.298:   29        |
|      3:    27.112 -  36.149:  129   |   8:    72.298 -  81.335:   14        |
|      4:    36.149 -  45.186:  123   |   9:    81.335 -  90.372:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1597             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1596             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1596   ksol= 0.33   Bsol= 59.69   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-1.84,-0.27,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166789                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8858 -  4.6802 0.99   1443  159 0.0987 0.1292      5.3934      5.5601|
|  2:  4.6802 -  3.7341 0.99   1396  154 0.0847 0.1075      5.4266      5.6135|
|  3:  3.7341 -  3.2678 0.99   1357  156 0.1076 0.1511      5.4705      5.8128|
|  4:  3.2678 -  2.9716 0.99   1351  140 0.1247 0.1529      5.4433      5.5942|
|  5:  2.9716 -  2.7600 0.99   1339  154 0.1317 0.1605      5.3316      5.5115|
|  6:  2.7600 -  2.5982 0.98   1331  148 0.1274 0.2126      5.2364      5.5213|
|  7:  2.5982 -  2.4687 0.99   1325  160 0.1282 0.1722      5.1912      5.3866|
|  8:  2.4687 -  2.3617 0.99   1344  138 0.1176 0.1732      5.0986      5.2868|
|  9:  2.3617 -  2.2711 0.98   1329  144 0.1165 0.1884      5.0285      5.3738|
| 10:  2.2711 -  2.1930 0.98   1306  143 0.1168 0.1800      4.9651      5.1772|
| 11:  2.1930 -  2.1246 0.98   1301  159 0.1179 0.1837      4.9251       5.274|
| 12:  2.1246 -  2.0640 0.99   1339  141 0.1190 0.1597      4.9005      5.0971|
| 13:  2.0640 -  2.0098 0.86   1157  118 0.1094 0.1835      4.7727      5.0282|
| 14:  2.0098 -  1.9609 0.24    312   45 0.0956 0.1637      4.6687       4.892|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8858 -  4.6802  1443   159  0.94   9.35   0.97     0.94       7373.96|
|  2:  4.6802 -  3.7341  1396   154  0.95   7.90   1.01     0.99       8889.42|
|  3:  3.7341 -  3.2678  1357   156  0.93  11.47   1.02     1.02      10164.26|
|  4:  3.2678 -  2.9716  1351   140  0.92  13.85   1.01     1.00      10083.54|
|  5:  2.9716 -  2.7600  1339   154  0.90  16.16   0.99     0.97       8641.76|
|  6:  2.7600 -  2.5982  1331   148  0.89  17.04   0.97     0.94       7375.67|
|  7:  2.5982 -  2.4687  1325   160  0.90  16.51   0.98     0.95       6730.21|
|  8:  2.4687 -  2.3617  1344   138  0.90  16.22   0.99     0.96       5888.51|
|  9:  2.3617 -  2.2711  1329   144  0.90  16.26   0.99     0.95       5130.87|
| 10:  2.2711 -  2.1930  1306   143  0.90  16.13   0.99     0.95       4495.92|
| 11:  2.1930 -  2.1246  1301   159  0.90  16.20   0.98     0.94       4240.49|
| 12:  2.1246 -  2.0640  1339   141  0.90  16.76   1.00     0.99       4165.29|
| 13:  2.0640 -  2.0098  1157   118  0.90  16.33   0.97     0.96       3353.46|
| 14:  2.0098 -  1.9609   312    45  0.92  13.13   0.97     0.93       2512.12|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2512.12 max =        10164.26 mean =      6644.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.34 mean =        14.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1596   ksol= 0.32   Bsol= 54.06   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.68,-0.14,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1596   ksol= 0.32   Bsol= 54.06   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.68,-0.14,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166916                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8858 -  4.6802 0.99   1443  159 0.0984 0.1290      5.3914      5.5581|
|  2:  4.6802 -  3.7341 0.99   1396  154 0.0843 0.1073      5.4241      5.6118|
|  3:  3.7341 -  3.2678 0.99   1357  156 0.1075 0.1511      5.4693      5.8128|
|  4:  3.2678 -  2.9716 0.99   1351  140 0.1249 0.1535      5.4445       5.596|
|  5:  2.9716 -  2.7600 0.99   1339  154 0.1319 0.1609      5.3333      5.5131|
|  6:  2.7600 -  2.5982 0.98   1331  148 0.1276 0.2131       5.238      5.5235|
|  7:  2.5982 -  2.4687 0.99   1325  160 0.1283 0.1722      5.1924      5.3872|
|  8:  2.4687 -  2.3617 0.99   1344  138 0.1177 0.1735      5.0993      5.2874|
|  9:  2.3617 -  2.2711 0.98   1329  144 0.1165 0.1883      5.0289      5.3738|
| 10:  2.2711 -  2.1930 0.98   1306  143 0.1168 0.1800      4.9654      5.1778|
| 11:  2.1930 -  2.1246 0.98   1301  159 0.1180 0.1838      4.9255      5.2743|
| 12:  2.1246 -  2.0640 0.99   1339  141 0.1190 0.1598      4.9005      5.0968|
| 13:  2.0640 -  2.0098 0.86   1157  118 0.1094 0.1837      4.7729      5.0287|
| 14:  2.0098 -  1.9609 0.24    312   45 0.0956 0.1636      4.6695      4.8919|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8858 -  4.6802  1443   159  0.94   9.33   0.97     0.95       7343.41|
|  2:  4.6802 -  3.7341  1396   154  0.95   7.89   1.01     1.00       8859.81|
|  3:  3.7341 -  3.2678  1357   156  0.93  11.45   1.03     1.02      10144.51|
|  4:  3.2678 -  2.9716  1351   140  0.92  13.87   1.01     1.00      10108.96|
|  5:  2.9716 -  2.7600  1339   154  0.90  16.19   1.00     0.98       8675.63|
|  6:  2.7600 -  2.5982  1331   148  0.89  17.08   0.98     0.95       7401.02|
|  7:  2.5982 -  2.4687  1325   160  0.90  16.54   0.99     0.96       6748.81|
|  8:  2.4687 -  2.3617  1344   138  0.90  16.23   1.00     0.97       5895.01|
|  9:  2.3617 -  2.2711  1329   144  0.90  16.27   1.00     0.96       5135.29|
| 10:  2.2711 -  2.1930  1306   143  0.90  16.14   0.99     0.95       4496.78|
| 11:  2.1930 -  2.1246  1301   159  0.90  16.21   0.99     0.95       4243.11|
| 12:  2.1246 -  2.0640  1339   141  0.90  16.77   1.00     1.00       4166.73|
| 13:  2.0640 -  2.0098  1157   118  0.90  16.34   0.98     0.96       3356.07|
| 14:  2.0098 -  1.9609   312    45  0.92  13.14   0.98     0.94       2516.23|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2516.23 max =        10144.51 mean =      6646.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.65 mean =        14.53|
|phase err.(test): min =        0.00 max =           89.39 mean =        14.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.826)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.38   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    90.38   16.85    None  None   None       |
|    Sol.    : 438    0      0.00    90.38   40.18    None  None   None       |
|    Mac.    : 2385   0      0.76    89.50   12.56    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:     0.003 -   9.040:  894   |   5:    45.189 -  54.226:   94        |
|      1:     9.040 -  18.077: 1227   |   6:    54.226 -  63.264:   62        |
|      2:    18.077 -  27.115:  245   |   7:    63.264 -  72.301:   29        |
|      3:    27.115 -  36.152:  129   |   8:    72.301 -  81.338:   14        |
|      4:    36.152 -  45.189:  123   |   9:    81.338 -  90.375:    6        |
|                               =>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: 0.518 - 4.363
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 281
   mapped sites are within: 0.703 - 4.363

peak=    5.459 closest distance to " CB  ARG A 275 " =    0.960
peak=    5.296 closest distance to " NH2 ARG A  56 " =    2.147
peak=    5.220 closest distance to " CG  PRO A  54 " =    1.350
peak=    4.804 closest distance to " NE2 GLN A  11 " =    1.089
peak=    4.746 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.700 closest distance to " O   HOH Z 126 " =    1.862
peak=    4.686 closest distance to " CG  PRO A  90 " =    1.276
peak=    4.667 closest distance to " CZ  PHE A 218 " =    1.126
peak=    4.544 closest distance to " O   HOH Z 403 " =    1.859
peak=    4.532 closest distance to " O   HOH Z 369 " =    2.240
peak=    4.467 closest distance to " CB  PRO A  54 " =    0.991
peak=    4.460 closest distance to " CB  SER A  63 " =    1.116
peak=    4.458 closest distance to " CD2 TRP A 179 " =    1.306
peak=    4.450 closest distance to " O   HOH Z 287 " =    1.823
peak=    4.445 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.433 closest distance to " CG  PRO A 213 " =    1.262
peak=    4.422 closest distance to " O   HOH Z 142 " =    1.612
peak=    4.406 closest distance to " CB  ARG A 190 " =    1.679
peak=    4.395 closest distance to " O   HOH Z 298 " =    1.836
peak=    4.393 closest distance to " ND2 ASN A 187 " =    1.567
peak=    4.347 closest distance to " O   HOH Z 402 " =    1.400
peak=    4.283 closest distance to " O   SER A  87 " =    2.223
peak=    4.266 closest distance to " CA  TYR A  30 " =    0.907
peak=    4.266 closest distance to " O   HOH Z 232 " =    2.387
peak=    4.262 closest distance to " O   HOH Z 406 " =    1.676
peak=    4.250 closest distance to " CA  ARG A  36 " =    1.028
peak=    4.248 closest distance to " O   HOH Z  40 " =    1.770
peak=    4.229 closest distance to " O   HOH Z  78 " =    1.746
peak=    4.220 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.209 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.191 closest distance to " CB  ARG A  79 " =    1.455
peak=    4.183 closest distance to " CB  ASN A 148 " =    1.440
peak=    4.178 closest distance to " ND2 ASN A 249 " =    0.922
peak=    4.129 closest distance to " O   HOH Z 250 " =    1.459
peak=    4.115 closest distance to " C   PRO A 198 " =    1.528
peak=    4.101 closest distance to " O  BHOH Z  74 " =    1.182
peak=    4.100 closest distance to " O   HOH Z 427 " =    3.051
peak=    4.097 closest distance to " O   HOH Z 188 " =    2.757
peak=    4.085 closest distance to " CB  GLU A 152 " =    1.154
peak=    4.059 closest distance to " O   HOH Z  63 " =    1.928
peak=    4.048 closest distance to " CG2 VAL A 257 " =    0.803
peak=    4.044 closest distance to " CB  GLU A 277 " =    3.632
peak=    4.042 closest distance to " O   HOH Z  44 " =    2.108
peak=    4.032 closest distance to " O   HOH Z  19 " =    1.936
peak=    4.029 closest distance to " O   HOH Z 234 " =    3.714
peak=    4.023 closest distance to " O   HOH Z 346 " =    1.621
peak=    4.011 closest distance to " CB  VAL A 265 " =    1.237
peak=    4.009 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.998 closest distance to " O   HOH Z  97 " =    2.056
peak=    3.995 closest distance to " O   HOH Z  43 " =    2.032
peak=    3.992 closest distance to " O   HOH Z  15 " =    2.236
peak=    3.989 closest distance to " O   HOH Z 132 " =    2.666
peak=    3.981 closest distance to " CB  ASN A 110 " =    1.110
peak=    3.975 closest distance to " O   HOH Z 248 " =    1.370
peak=    3.973 closest distance to " CE  LYS A  76 " =    0.912
peak=    3.967 closest distance to " O   HOH Z  78 " =    2.100
peak=    3.953 closest distance to " CZ3 TRP A 266 " =    1.107
peak=    3.947 closest distance to " NH1AARG A 145 " =    1.371
peak=    3.938 closest distance to " CB  VAL A 202 " =    1.548
peak=    3.933 closest distance to " CG  ARG A  66 " =    2.416
peak=    3.931 closest distance to " O   ASN A  74 " =    1.369
peak=    3.918 closest distance to " O   HOH Z 227 " =    1.613
peak=    3.910 closest distance to " CB  GLU A  46 " =    1.035
peak=    3.908 closest distance to " O   HOH Z 209 " =    2.282
peak=    3.897 closest distance to " O   HOH Z 180 " =    2.180
peak=    3.897 closest distance to " NZ  LYS A 117 " =    3.089
peak=    3.890 closest distance to " O   HOH Z 327 " =    1.572
peak=    3.863 closest distance to " O   HOH Z 303 " =    2.169
peak=    3.853 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.844 closest distance to " O   HOH Z 128 " =    2.302
peak=    3.840 closest distance to " O   HOH Z 188 " =    1.481
peak=    3.832 closest distance to " CG2 ILE A 120 " =    1.295
peak=    3.830 closest distance to " O  BHOH Z 338 " =    2.262
peak=    3.830 closest distance to " CZ  PHE A  38 " =    1.199
peak=    3.822 closest distance to " O   HOH Z 368 " =    3.674
peak=    3.818 closest distance to " O   HOH Z 411 " =    3.928
peak=    3.811 closest distance to " CG  GLU A  37 " =    1.027
peak=    3.805 closest distance to " O   HOH Z 368 " =    2.134
peak=    3.791 closest distance to " CB  PRO A  90 " =    1.087
peak=    3.790 closest distance to " CD  LYS A  76 " =    1.980
peak=    3.785 closest distance to " O   HOH Z 353 " =    2.609
peak=    3.767 closest distance to " CB  SER A  26 " =    1.855
peak=    3.749 closest distance to " CB  TRP A 266 " =    1.083
peak=    3.743 closest distance to " CB  ARG A  79 " =    0.929
peak=    3.741 closest distance to " NH2AARG A 190 " =    2.090
peak=    3.729 closest distance to " CB  ASN A 142 " =    1.087
peak=    3.723 closest distance to " OG ASER A 258 " =    3.097
peak=    3.718 closest distance to " N   ASN A  39 " =    1.240
peak=    3.715 closest distance to " O   HOH Z 365 " =    2.714
peak=    3.713 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.703 closest distance to " CA  ARG A 195 " =    1.234
peak=    3.703 closest distance to " CA  ASN A 215 " =    1.017
peak=    3.698 closest distance to " N   TYR A 116 " =    1.576
peak=    3.691 closest distance to " O   HOH Z 193 " =    1.535
peak=    3.689 closest distance to " N   ARG A 156 " =    1.363
peak=    3.682 closest distance to " NH2BARG A 145 " =    2.073
peak=    3.676 closest distance to " CB  THR A  31 " =    1.571
peak=    3.672 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.662 closest distance to " CG2AVAL A 121 " =    2.238
peak=    3.645 closest distance to " O   HOH Z 265 " =    2.128
peak=    3.644 closest distance to " O   HOH Z  59 " =    2.017
peak=    3.637 closest distance to " O   HOH Z 280 " =    3.007
peak=    3.635 closest distance to " O   HOH Z  88 " =    2.630
peak=    3.630 closest distance to " CG  MET A 185 " =    1.093
peak=    3.626 closest distance to " O   THR A 220 " =    1.162
peak=    3.620 closest distance to " CB  PHE A 204 " =    0.749
peak=    3.620 closest distance to " CA  ALA A  51 " =    0.963
peak=    3.618 closest distance to " CB  GLN A  89 " =    1.381
peak=    3.618 closest distance to " O   HOH Z 158 " =    3.061
peak=    3.611 closest distance to " CD2 LEU A 297 " =    1.015
peak=    3.595 closest distance to " O   HOH Z 325 " =    2.358
peak=    3.591 closest distance to " CG  GLN A  58 " =    0.884
peak=    3.589 closest distance to " CG  GLN A  11 " =    1.886
peak=    3.587 closest distance to " N   PHE A 130 " =    1.260
peak=    3.580 closest distance to " O   HOH Z 214 " =    2.378
peak=    3.577 closest distance to " CB  SER A  62 " =    1.007
peak=    3.575 closest distance to " CB  TRP A 179 " =    1.371
peak=    3.573 closest distance to " CA  ALA A 154 " =    0.961
peak=    3.568 closest distance to " O   HOH Z  61 " =    1.649
peak=    3.561 closest distance to " OG BSER A 164 " =    2.249
peak=    3.558 closest distance to " O   HOH Z  21 " =    1.844
peak=    3.557 closest distance to " O   HOH Z 251 " =    1.672
peak=    3.553 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.550 closest distance to " O   HOH Z 128 " =    1.885
peak=    3.546 closest distance to " O   HOH Z 261 " =    2.158
peak=    3.546 closest distance to " CA  SER A  87 " =    1.030
peak=    3.546 closest distance to " O   THR A 182 " =    1.449
peak=    3.535 closest distance to " CB  LEU A  83 " =    0.703
peak=    3.533 closest distance to " CB  ALA A 114 " =    1.017
peak=    3.531 closest distance to " O   HOH Z 185 " =    1.820
peak=    3.530 closest distance to " O   HOH Z 389 " =    1.759
peak=    3.524 closest distance to " CB  LEU A 228 " =    1.128
peak=    3.523 closest distance to " CB  SER A   3 " =    1.305
peak=    3.513 closest distance to " CD1 ILE A 199 " =    1.169
peak=    3.512 closest distance to " O   HOH Z  97 " =    2.070
peak=    3.511 closest distance to " O   HOH Z 425 " =    1.300
peak=    3.509 closest distance to " CG  LEU A 167 " =    1.260
peak=    3.509 closest distance to " O   HOH Z 203 " =    1.720
peak=    3.502 closest distance to " O   HOH Z 394 " =    3.796
peak=    3.501 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.499 closest distance to " CA  THR A 264 " =    0.892
peak=    3.495 closest distance to " CA  ALA A  84 " =    1.211
peak=    3.489 closest distance to " O   HOH Z 438 " =    3.031
peak=    3.483 closest distance to " O   HOH Z 337 " =    3.583
peak=    3.480 closest distance to " CA  VAL A 125 " =    1.154
peak=    3.476 closest distance to " O   HOH Z 357 " =    2.048
peak=    3.473 closest distance to " CB  GLU A 128 " =    1.006
peak=    3.470 closest distance to " CE  LYS A 119 " =    1.115
peak=    3.469 closest distance to " O   HOH Z 421 " =    1.580
peak=    3.469 closest distance to " O   HOH Z 392 " =    2.707
peak=    3.468 closest distance to " O   HOH Z 173 " =    1.939
peak=    3.467 closest distance to " CB  THR A  52 " =    0.741
peak=    3.465 closest distance to " CD  ARG A 159 " =    0.726
peak=    3.462 closest distance to " O   HOH Z  54 " =    1.681
peak=    3.461 closest distance to " O   HOH Z 371 " =    3.066
peak=    3.458 closest distance to " O   HOH Z  68 " =    2.046
peak=    3.451 closest distance to " CD1 LEU A  96 " =    0.738
peak=    3.450 closest distance to " O   HOH Z 419 " =    2.074
peak=    3.449 closest distance to " O   HOH Z 163 " =    2.041
peak=    3.447 closest distance to " CE1 TYR A 186 " =    1.246
peak=    3.442 closest distance to " O   HOH Z  62 " =    2.210
peak=    3.428 closest distance to " O   HOH Z 417 " =    3.410
peak=    3.428 closest distance to " CB  ALA A 291 " =    1.035
peak=    3.423 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.420 closest distance to " O   HOH Z 109 " =    1.263
peak=    3.419 closest distance to " O   HOH Z 422 " =    2.593
peak=    3.413 closest distance to " O   HOH Z 291 " =    1.428
peak=    3.408 closest distance to " O   HOH Z 285 " =    2.317
peak=    3.405 closest distance to " O   HOH Z 359 " =    1.614
peak=    3.401 closest distance to " O   ALA A 165 " =    1.522
peak=    3.399 closest distance to " CA  TYR A 116 " =    1.383
peak=    3.399 closest distance to " O   HOH Z   1 " =    1.983
peak=    3.396 closest distance to " OH  TYR A 116 " =    1.116
peak=    3.395 closest distance to " O   HOH Z 106 " =    4.169
peak=    3.394 closest distance to " OD1 ASN A  69 " =    2.492
peak=    3.392 closest distance to " N   ASP A 162 " =    1.190
peak=    3.388 closest distance to " CA  SER A  32 " =    1.708
peak=    3.372 closest distance to " CB  PRO A 198 " =    1.243
peak=    3.372 closest distance to " CA  ASN A 127 " =    1.206
peak=    3.370 closest distance to " O   HOH Z 166 " =    3.990
peak=    3.370 closest distance to " CG AARG A 275 " =    1.152
peak=    3.368 closest distance to " CB  ALA A 248 " =    1.350
peak=    3.367 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.362 closest distance to " O   TYR A 116 " =    1.432
peak=    3.349 closest distance to " O   HOH Z 299 " =    4.363
peak=    3.349 closest distance to " CA  ASN A 217 " =    1.242
peak=    3.347 closest distance to " CG1 ILE A  33 " =    1.208
peak=    3.347 closest distance to " CB  SER A 212 " =    1.246
peak=    3.346 closest distance to " CB  GLN A  88 " =    1.139
peak=    3.335 closest distance to " CG2 ILE A  20 " =    1.395
peak=    3.325 closest distance to " CA  ASP A 124 " =    0.791
peak=    3.323 closest distance to " O   HOH Z 305 " =    3.710
peak=    3.322 closest distance to " CB  LEU A 300 " =    0.941
peak=    3.320 closest distance to " O   HOH Z 298 " =    2.261
peak=    3.317 closest distance to " CB  PRO A 243 " =    1.235
peak=    3.311 closest distance to " O   HOH Z 258 " =    2.107
peak=    3.310 closest distance to " O   HOH Z 148 " =    3.427
peak=    3.308 closest distance to " O   HOH Z 361 " =    2.514
peak=    3.295 closest distance to " CB  SER A 210 " =    0.803
peak=    3.293 closest distance to " O   HOH Z  47 " =    1.881
peak=    3.290 closest distance to " CB  ASP A 298 " =    1.159
peak=    3.290 closest distance to " O   HOH Z  63 " =    2.298
peak=    3.288 closest distance to " OG1 THR A 264 " =    0.750
peak=    3.286 closest distance to " O   HOH Z 172 " =    3.878
peak=    3.282 closest distance to " O   HOH Z  88 " =    3.048
peak=    3.274 closest distance to " O   HOH Z 417 " =    1.003
peak=    3.263 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.262 closest distance to " O   HOH Z  78 " =    2.126
peak=    3.258 closest distance to " CB  HIS A 108 " =    0.839
peak=    3.257 closest distance to " O   HOH Z  80 " =    1.730
peak=    3.253 closest distance to " O   HOH Z 345 " =    1.640
peak=    3.250 closest distance to " CG2AVAL A  72 " =    1.731
peak=    3.247 closest distance to " CD  PRO A  54 " =    0.996
peak=    3.246 closest distance to " O   HOH Z 193 " =    1.863
peak=    3.246 closest distance to " CA  MET A 105 " =    1.020
peak=    3.243 closest distance to " CA  ALA A 100 " =    0.995
peak=    3.242 closest distance to " O   HOH Z 250 " =    1.542
peak=    3.236 closest distance to " CG2 THR A 221 " =    1.124
peak=    3.233 closest distance to " CA  ALA A 158 " =    1.308
peak=    3.232 closest distance to " CD1AILE A 234 " =    0.878
peak=    3.231 closest distance to " CG1 ILE A 120 " =    1.028
peak=    3.230 closest distance to " CB  SER A 141 " =    1.125
peak=    3.225 closest distance to " O   HOH Z 227 " =    2.101
peak=    3.222 closest distance to " CB  TYR A 116 " =    0.780
peak=    3.218 closest distance to " CA  ASP A 149 " =    1.286
peak=    3.217 closest distance to " O   HOH Z 234 " =    2.252
peak=    3.216 closest distance to " O   HOH Z 332 " =    1.518
peak=    3.216 closest distance to " O   HOH Z 250 " =    2.165
peak=    3.207 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.205 closest distance to " CA  GLN A  94 " =    0.780
peak=    3.200 closest distance to " CB  ALA A 242 " =    1.006
peak=    3.195 closest distance to " O   HOH Z  10 " =    1.703
peak=    3.195 closest distance to " CB  SER A 273 " =    0.832
peak=    3.194 closest distance to " O   HOH Z 407 " =    2.812
peak=    3.193 closest distance to " CD2 TYR A 186 " =    1.078
peak=    3.193 closest distance to " O   HOH Z 313 " =    1.346
peak=    3.193 closest distance to " O   HOH Z 345 " =    3.110
peak=    3.190 closest distance to " CB  PHE A  16 " =    1.106
peak=    3.184 closest distance to " CG2 VAL A 197 " =    1.077
peak=    3.180 closest distance to " CA  ARG A 159 " =    1.273
peak=    3.179 closest distance to " OG ASER A  99 " =    1.403
peak=    3.177 closest distance to " OG BSER A  99 " =    2.759
peak=    3.175 closest distance to " O   HOH Z  49 " =    0.884
peak=    3.172 closest distance to " CB  SER A  62 " =    1.347
peak=    3.170 closest distance to " CB  ILE A 120 " =    1.282
peak=    3.169 closest distance to " O   HOH Z  28 " =    1.797
peak=    3.168 closest distance to " CA  TRP A  85 " =    1.123
peak=    3.161 closest distance to " CB  ALA A 227 " =    1.281
peak=    3.160 closest distance to " CG  GLN A  55 " =    2.393
peak=    3.157 closest distance to " CB  ASN A 285 " =    0.976
peak=    3.154 closest distance to " O   HOH Z 334 " =    1.320
peak=    3.147 closest distance to " OG  SER A  22 " =    2.604
peak=    3.144 closest distance to " CB  ARG A 219 " =    0.858
peak=    3.140 closest distance to " N   HIS A 108 " =    1.731
peak=    3.138 closest distance to " O   HOH Z 371 " =    1.532
peak=    3.135 closest distance to " CA  ASP A 140 " =    1.212
peak=    3.116 closest distance to " CA  ALA A  21 " =    1.117
peak=    3.115 closest distance to " O   HOH Z 294 " =    1.485
peak=    3.115 closest distance to " CB  ASP A 191 " =    1.215
peak=    3.114 closest distance to " OE1 GLU A   2 " =    2.181
peak=    3.105 closest distance to " CD  ARG A  66 " =    2.545
peak=    3.093 closest distance to " CG1AVAL A 121 " =    0.752
peak=    3.092 closest distance to " O   HOH Z 193 " =    1.580
peak=    3.090 closest distance to " CA  SER A 146 " =    1.929
peak=    3.090 closest distance to " OG1 THR A 221 " =    1.258
peak=    3.080 closest distance to " OD2 ASP A 286 " =    3.223
peak=    3.078 closest distance to " N   ASN A 127 " =    1.269
peak=    3.074 closest distance to " O   HOH Z  48 " =    1.597
peak=    3.071 closest distance to " CB  ARG A 138 " =    0.793
peak=    3.070 closest distance to " O   HOH Z  85 " =    2.165
peak=    3.054 closest distance to " OE2 GLU A  53 " =    1.331
peak=    3.051 closest distance to " CB  ALA A 104 " =    0.729
peak=    3.048 closest distance to " OG  SER A 245 " =    1.607
peak=    3.016 closest distance to " O   HOH Z  30 " =    2.352

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.827 - 5.917
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.827 - 5.917

peak=   -4.849 closest distance to " CD  ARG A  14 " =    3.379
peak=   -4.702 closest distance to " CG  GLN A  58 " =    1.057
peak=   -4.556 closest distance to " OG BSER A 134 " =    1.281
peak=   -4.537 closest distance to " CG2 ILE A  49 " =    2.800
peak=   -4.519 closest distance to " C   HIS A 108 " =    1.116
peak=   -4.358 closest distance to " O   PRO A 198 " =    1.276
peak=   -4.346 closest distance to " O   HOH Z 266 " =    5.505
peak=   -4.292 closest distance to " CB  PRO A 243 " =    2.748
peak=   -4.245 closest distance to " O   HOH Z 198 " =    1.238
peak=   -4.182 closest distance to " CD2 TYR A 293 " =    1.906
peak=   -4.170 closest distance to " CA  VAL A  67 " =    2.960
peak=   -4.167 closest distance to " CE  MET A 105 " =    2.524
peak=   -4.145 closest distance to " CG1 VAL A 112 " =    2.798
peak=   -4.118 closest distance to " CD  ARG A 156 " =    2.145
peak=   -4.029 closest distance to " O   HOH Z 377 " =    2.070
peak=   -3.996 closest distance to " O   HOH Z 231 " =    2.343
peak=   -3.995 closest distance to " CD1 LEU A 101 " =    2.410
peak=   -3.981 closest distance to " OXT GLY A 302 " =    2.930
peak=   -3.926 closest distance to " CD2 PHE A 192 " =    2.113
peak=   -3.912 closest distance to " O   HOH Z 193 " =    1.317
peak=   -3.878 closest distance to " N   ALA A 248 " =    1.766
peak=   -3.861 closest distance to " O   HOH Z 290 " =    1.124
peak=   -3.847 closest distance to " OE1 GLN A 223 " =    2.193
peak=   -3.840 closest distance to " CB  ASN A  39 " =    2.361
peak=   -3.809 closest distance to " OG  SER A  97 " =    2.246
peak=   -3.787 closest distance to " OD2 ASP A 191 " =    1.424
peak=   -3.778 closest distance to " CE2 TYR A  30 " =    2.762
peak=   -3.776 closest distance to " O   HOH Z   6 " =    2.164
peak=   -3.760 closest distance to " O   HOH Z 211 " =    1.341
peak=   -3.756 closest distance to " O   VAL A 174 " =    2.241
peak=   -3.736 closest distance to " O   VAL A  67 " =    2.562
peak=   -3.729 closest distance to " O   SER A 210 " =    2.057
peak=   -3.713 closest distance to " O   HOH Z 102 " =    1.638
peak=   -3.705 closest distance to " O   HOH Z 348 " =    2.238
peak=   -3.690 closest distance to " CA  GLY A 241 " =    2.392
peak=   -3.684 closest distance to " CZ3 TRP A 179 " =    1.293
peak=   -3.679 closest distance to " NE2 GLN A  11 " =    1.715
peak=   -3.672 closest distance to " O   PRO A 163 " =    2.021
peak=   -3.662 closest distance to " O   HOH Z 196 " =    1.967
peak=   -3.654 closest distance to " ND2 ASN A 249 " =    2.315
peak=   -3.651 closest distance to " CZ  TYR A 169 " =    1.884
peak=   -3.643 closest distance to " CE BMET A  47 " =    1.332
peak=   -3.635 closest distance to " CD1 LEU A  25 " =    2.541
peak=   -3.628 closest distance to " CD2 TYR A 247 " =    2.388
peak=   -3.627 closest distance to " O   HOH Z 165 " =    1.971
peak=   -3.627 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.618 closest distance to " O   HOH Z 185 " =    2.365
peak=   -3.615 closest distance to " O   HOH Z 351 " =    1.458
peak=   -3.597 closest distance to " O   HOH Z 394 " =    1.484
peak=   -3.591 closest distance to " OE1 GLN A 183 " =    1.542
peak=   -3.588 closest distance to " CE2 PHE A  61 " =    2.638
peak=   -3.580 closest distance to " O   HOH Z 166 " =    1.907
peak=   -3.568 closest distance to " CD  PRO A 243 " =    2.081
peak=   -3.567 closest distance to " O   HOH Z 198 " =    0.827
peak=   -3.564 closest distance to " N   THR A  52 " =    1.729
peak=   -3.553 closest distance to " CG1 VAL A 112 " =    2.601
peak=   -3.552 closest distance to " O   ALA A  10 " =    1.710
peak=   -3.541 closest distance to " CB  TRP A  85 " =    2.570
peak=   -3.538 closest distance to " CG1 VAL A 250 " =    2.616
peak=   -3.514 closest distance to " CB  ALA A 248 " =    2.245
peak=   -3.514 closest distance to " CG  PHE A 283 " =    2.622
peak=   -3.512 closest distance to " CZ  TYR A 172 " =    1.890
peak=   -3.498 closest distance to " CE3 TRP A 150 " =    2.341
peak=   -3.495 closest distance to " O   HOH Z  63 " =    1.568
peak=   -3.492 closest distance to " O   PHE A 218 " =    1.560
peak=   -3.486 closest distance to " CD2 HIS A 207 " =    2.407
peak=   -3.486 closest distance to " CB  ALA A  43 " =    2.495
peak=   -3.482 closest distance to " OD2 ASP A 171 " =    2.420
peak=   -3.477 closest distance to " CD  ARG A  79 " =    1.169
peak=   -3.476 closest distance to " O   ALA A 292 " =    2.199
peak=   -3.476 closest distance to " O   HOH Z 281 " =    2.685
peak=   -3.475 closest distance to " ND2 ASN A 187 " =    1.599
peak=   -3.472 closest distance to " N   ASP A 286 " =    2.177
peak=   -3.460 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.459 closest distance to " OD1 ASP A 171 " =    1.487
peak=   -3.445 closest distance to " O   ILE A 109 " =    2.549
peak=   -3.443 closest distance to " N   ALA A 248 " =    2.218
peak=   -3.442 closest distance to " O   VAL A 189 " =    1.741
peak=   -3.440 closest distance to " O   HOH Z 374 " =    1.825
peak=   -3.439 closest distance to " NH2 ARG A  66 " =    1.095
peak=   -3.435 closest distance to " ND2 ASN A  45 " =    1.903
peak=   -3.428 closest distance to " CG1 VAL A 265 " =    2.672
peak=   -3.417 closest distance to " CZ3 TRP A 274 " =    2.367
peak=   -3.409 closest distance to " CG  GLU A  53 " =    1.495
peak=   -3.408 closest distance to " O   ALA A  34 " =    2.219
peak=   -3.405 closest distance to " O   HOH Z 114 " =    3.247
peak=   -3.400 closest distance to " O   TRP A  92 " =    1.868
peak=   -3.397 closest distance to " O   HOH Z 421 " =    3.444
peak=   -3.393 closest distance to " O   HOH Z 216 " =    1.427
peak=   -3.392 closest distance to " SD  MET A 105 " =    1.023
peak=   -3.389 closest distance to " CB  ALA A  10 " =    2.317
peak=   -3.387 closest distance to " CG2 ILE A 263 " =    2.231
peak=   -3.386 closest distance to " CA  GLY A 241 " =    3.221
peak=   -3.385 closest distance to " CD  ARG A 195 " =    5.165
peak=   -3.384 closest distance to " O   HOH Z  13 " =    1.852
peak=   -3.384 closest distance to " O   HOH Z 111 " =    3.801
peak=   -3.376 closest distance to " O   HOH Z 357 " =    2.129
peak=   -3.372 closest distance to " O   HOH Z 283 " =    2.497
peak=   -3.364 closest distance to " O   ASN A 252 " =    1.343
peak=   -3.359 closest distance to " O   HOH Z 110 " =    1.363
peak=   -3.357 closest distance to " CG  TRP A 266 " =    1.947
peak=   -3.355 closest distance to " OD1 ASP A 191 " =    1.470
peak=   -3.353 closest distance to " CA  ILE A 263 " =    1.053
peak=   -3.349 closest distance to " OD1 ASN A 148 " =    1.428
peak=   -3.347 closest distance to " OG BSER A 134 " =    1.902
peak=   -3.342 closest distance to " O   HOH Z   6 " =    1.610
peak=   -3.338 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.336 closest distance to " OE1 GLN A  88 " =    1.064
peak=   -3.332 closest distance to " CG  LEU A  83 " =    2.066
peak=   -3.323 closest distance to " O   HOH Z 301 " =    2.394
peak=   -3.321 closest distance to " O   GLY A  80 " =    2.510
peak=   -3.317 closest distance to " CZ  ARG A 259 " =    0.958
peak=   -3.311 closest distance to " CG  GLU A 277 " =    1.344
peak=   -3.307 closest distance to " O   HOH Z 252 " =    4.042
peak=   -3.307 closest distance to " O   HOH Z 407 " =    2.735
peak=   -3.305 closest distance to " O   HOH Z 174 " =    2.451
peak=   -3.303 closest distance to " CG1AVAL A  41 " =    2.551
peak=   -3.303 closest distance to " CG  ARG A 269 " =    2.248
peak=   -3.302 closest distance to " O   SER A  95 " =    1.607
peak=   -3.296 closest distance to " CD1 ILE A 106 " =    2.278
peak=   -3.293 closest distance to " NE2 GLN A  88 " =    1.128
peak=   -3.292 closest distance to " O   HOH Z  60 " =    1.651
peak=   -3.288 closest distance to " O   HOH Z 372 " =    2.296
peak=   -3.286 closest distance to " CG1BVAL A  41 " =    2.876
peak=   -3.286 closest distance to " NE2 GLN A 278 " =    1.726
peak=   -3.284 closest distance to " CD  GLN A 223 " =    1.673
peak=   -3.283 closest distance to " NH2 ARG A  79 " =    1.559
peak=   -3.281 closest distance to " O   HOH Z 113 " =    1.672
peak=   -3.280 closest distance to " O   HOH Z 285 " =    1.522
peak=   -3.276 closest distance to " N   ALA A  43 " =    2.516
peak=   -3.275 closest distance to " O   HOH Z  38 " =    1.780
peak=   -3.274 closest distance to " CG  ASP A 132 " =    2.309
peak=   -3.270 closest distance to " O   HOH Z 197 " =    2.203
peak=   -3.264 closest distance to " O   HOH Z 131 " =    4.104
peak=   -3.263 closest distance to " O   HOH Z 264 " =    1.714
peak=   -3.263 closest distance to " O   HOH Z 111 " =    1.913
peak=   -3.261 closest distance to " CA  GLY A 133 " =    2.319
peak=   -3.260 closest distance to " O   ALA A 227 " =    1.401
peak=   -3.255 closest distance to " O   HOH Z  71 " =    2.525
peak=   -3.250 closest distance to " O   GLU A 152 " =    1.380
peak=   -3.245 closest distance to " OD1 ASN A 301 " =    1.901
peak=   -3.243 closest distance to " O   HOH Z 359 " =    2.966
peak=   -3.237 closest distance to " CG1 VAL A  78 " =    2.790
peak=   -3.231 closest distance to " O   HOH Z 297 " =    2.604
peak=   -3.231 closest distance to " O   HOH Z 353 " =    2.239
peak=   -3.227 closest distance to " O   HOH Z 243 " =    2.061
peak=   -3.219 closest distance to " O   HOH Z 177 " =    1.654
peak=   -3.218 closest distance to " O   HOH Z 116 " =    1.789
peak=   -3.214 closest distance to " CB  ALA A 291 " =    2.397
peak=   -3.211 closest distance to " O   HOH Z 313 " =    1.981
peak=   -3.211 closest distance to " O   HOH Z 265 " =    2.400
peak=   -3.210 closest distance to " CG2BVAL A  41 " =    1.153
peak=   -3.210 closest distance to " O   HOH Z 200 " =    4.869
peak=   -3.207 closest distance to " O   ILE A 106 " =    1.773
peak=   -3.205 closest distance to " CG  HIS A  86 " =    1.165
peak=   -3.205 closest distance to " CG2 THR A 178 " =    2.460
peak=   -3.193 closest distance to " CB  ASP A 286 " =    1.810
peak=   -3.187 closest distance to " C   LEU A 143 " =    0.999
peak=   -3.184 closest distance to " O   HOH Z 278 " =    1.265
peak=   -3.183 closest distance to " N   ALA A 226 " =    1.957
peak=   -3.179 closest distance to " NH2AARG A 275 " =    5.096
peak=   -3.176 closest distance to " O   ALA A   1 " =    1.817
peak=   -3.170 closest distance to " CG  PRO A 243 " =    1.762
peak=   -3.168 closest distance to " O   HOH Z 405 " =    2.632
peak=   -3.167 closest distance to " ND2 ASN A  60 " =    1.335
peak=   -3.165 closest distance to " NZ  LYS A 166 " =    1.245
peak=   -3.163 closest distance to " CA  GLY A 203 " =    2.329
peak=   -3.162 closest distance to " O   SER A 276 " =    1.669
peak=   -3.162 closest distance to " O   HOH Z 106 " =    1.932
peak=   -3.161 closest distance to " CG1 VAL A  67 " =    3.041
peak=   -3.160 closest distance to " ND2 ASN A  39 " =    1.170
peak=   -3.160 closest distance to " N   SER A 276 " =    1.371
peak=   -3.153 closest distance to " CD1 LEU A 255 " =    2.748
peak=   -3.149 closest distance to " O   HOH Z  10 " =    1.454
peak=   -3.149 closest distance to " CZ  PHE A  38 " =    2.013
peak=   -3.148 closest distance to " O   HOH Z 174 " =    3.688
peak=   -3.141 closest distance to " O   HOH Z 191 " =    5.917
peak=   -3.139 closest distance to " OH  TYR A 169 " =    0.926
peak=   -3.137 closest distance to " CD2 PHE A  61 " =    2.364
peak=   -3.133 closest distance to " O   HOH Z  37 " =    1.813
peak=   -3.130 closest distance to " OD1 ASN A  39 " =    2.285
peak=   -3.115 closest distance to " NH1 ARG A 195 " =    2.657
peak=   -3.113 closest distance to " CA  GLY A 133 " =    1.972
peak=   -3.110 closest distance to " CA  SER A 135 " =    1.261
peak=   -3.102 closest distance to " O   HOH Z  51 " =    2.062
peak=   -3.102 closest distance to " O   HOH Z  33 " =    2.843
peak=   -3.086 closest distance to " NE2 GLN A  88 " =    1.799
peak=   -3.076 closest distance to " O   HOH Z  64 " =    1.521
peak=   -3.073 closest distance to " O   HOH Z 364 " =    5.170
peak=   -3.046 closest distance to " CD  ARG A 139 " =    1.540
peak=   -3.040 closest distance to " O   HOH Z 318 " =    1.972
peak=   -3.039 closest distance to " CB  PHE A  16 " =    2.504
peak=   -3.026 closest distance to " C   GLY A  17 " =    0.968

================= 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    :  0.4090 0.4069   6.203098e+00   6.192512e+00
   1_bss:  0.3989 0.3962   6.189660e+00   6.178281e+00
   1_xyz:  0.2809 0.3058   5.905644e+00   5.984802e+00
   1_adp:  0.2588 0.3102   5.857742e+00   6.000473e+00
   1_occ:  0.2584 0.3102   5.857354e+00   6.001304e+00
   2_bss:  0.2559 0.3077   5.852606e+00   5.998009e+00
   2_xyz:  0.1696 0.2149   5.490227e+00   5.679895e+00
   2_adp:  0.1502 0.2024   5.396648e+00   5.613159e+00
   2_occ:  0.1501 0.2024   5.396046e+00   5.613058e+00
   3_bss:  0.1500 0.2013   5.392708e+00   5.607960e+00
   3_xyz:  0.1283 0.1720   5.255091e+00   5.473017e+00
   3_adp:  0.1239 0.1696   5.233217e+00   5.455466e+00
   3_occ:  0.1238 0.1696   5.232849e+00   5.455285e+00
   4_bss:  0.1237 0.1695   5.232399e+00   5.454872e+00
   4_xyz:  0.1177 0.1629   5.189209e+00   5.416777e+00
   4_adp:  0.1165 0.1622   5.184243e+00   5.414604e+00
   4_occ:  0.1165 0.1622   5.183665e+00   5.414023e+00
   5_bss:  0.1164 0.1619   5.183025e+00   5.411149e+00
   5_xyz:  0.1138 0.1609   5.171663e+00   5.407182e+00
   5_adp:  0.1135 0.1597   5.167336e+00   5.401279e+00
   5_occ:  0.1134 0.1596   5.166789e+00   5.401107e+00
   5_bss:  0.1133 0.1596   5.166916e+00   5.401389e+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:  0.316  36.866  -0.511  -2.220   3.672  -0.000   0.000   0.000
   1_xyz:  0.316  36.866  -0.511  -2.220   3.672  -0.000   0.000   0.000
   1_adp:  0.316  36.866  -0.511  -2.220   3.672  -0.000   0.000   0.000
   1_occ:  0.316  36.866  -0.511  -2.220   3.672  -0.000   0.000   0.000
   2_bss:  0.331  52.466  -2.118  -2.021   1.191  -0.000   0.000   0.000
   2_xyz:  0.331  52.466  -2.118  -2.021   1.191  -0.000   0.000   0.000
   2_adp:  0.331  52.466  -2.118  -2.021   1.191  -0.000   0.000   0.000
   2_occ:  0.331  52.466  -2.118  -2.021   1.191  -0.000   0.000   0.000
   3_bss:  0.321  59.689  -2.837  -2.010   0.033  -0.000   0.000   0.000
   3_xyz:  0.321  59.689  -2.837  -2.010   0.033  -0.000   0.000   0.000
   3_adp:  0.321  59.689  -2.837  -2.010   0.033  -0.000   0.000   0.000
   3_occ:  0.321  59.689  -2.837  -2.010   0.033  -0.000   0.000   0.000
   4_bss:  0.328  59.689  -2.956  -2.003  -0.330  -0.000  -0.000  -0.000
   4_xyz:  0.328  59.689  -2.956  -2.003  -0.330  -0.000  -0.000  -0.000
   4_adp:  0.328  59.689  -2.956  -2.003  -0.330  -0.000  -0.000  -0.000
   4_occ:  0.328  59.689  -2.956  -2.003  -0.330  -0.000  -0.000  -0.000
   5_bss:  0.328  59.689  -2.821  -1.841  -0.270  -0.000  -0.000  -0.000
   5_xyz:  0.328  59.689  -2.821  -1.841  -0.270  -0.000  -0.000  -0.000
   5_adp:  0.328  59.689  -2.821  -1.841  -0.270  -0.000  -0.000  -0.000
   5_occ:  0.328  59.689  -2.821  -1.841  -0.270  -0.000  -0.000  -0.000
   5_bss:  0.320  54.064  -2.677  -1.681  -0.145  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.311 0.5801  0.7583    49236.685
   1_bss:  44.030 0.5943  0.7922    46084.320
   1_xyz:  31.499 0.7421  0.9446    25272.020
   1_adp:  32.296 0.7325  0.9302    26303.467
   1_occ:  32.342 0.7320  0.9293    26362.663
   2_bss:  32.033 0.7355  0.8924    25998.806
   2_xyz:  21.083 0.8505  0.9872    11841.344
   2_adp:  19.204 0.8693  0.9949    10425.090
   2_occ:  19.195 0.8694  0.9949    10415.429
   3_bss:  19.016 0.8710  0.9736    10263.151
   3_xyz:  16.048 0.8974  0.9822     7650.280
   3_adp:  15.672 0.9010  0.9756     7458.794
   3_occ:  15.665 0.9010  0.9756     7451.527
   4_bss:  15.649 0.9012  0.9704     7445.726
   4_xyz:  14.797 0.9084  0.9744     6856.417
   4_adp:  14.734 0.9091  0.9684     6843.421
   4_occ:  14.722 0.9092  0.9684     6832.794
   5_bss:  14.687 0.9095  0.9724     6791.192
   5_xyz:  14.603 0.9101  0.9730     6728.467
   5_adp:  14.478 0.9112  0.9675     6648.375
   5_occ:  14.476 0.9112  0.9674     6643.384
   5_bss:  14.485 0.9111  0.9721     6646.295
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9470e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9470e-01
   1_xyz:   1.311  0.009  0.078 15.059  0.005  4.111   9.2360e-02
   1_adp:   1.311  0.009  0.078 15.059  0.005  4.111   9.2360e-02
   1_occ:   1.311  0.009  0.078 15.059  0.005  4.111   9.2360e-02
   2_bss:   1.311  0.009  0.078 15.059  0.005  4.111   9.2360e-02
   2_xyz:   1.135  0.008  0.077 14.912  0.004  4.126   7.1607e-02
   2_adp:   1.135  0.008  0.077 14.912  0.004  4.126   7.1607e-02
   2_occ:   1.135  0.008  0.077 14.912  0.004  4.126   7.1607e-02
   3_bss:   1.135  0.008  0.077 14.912  0.004  4.126   7.1607e-02
   3_xyz:   0.979  0.007  0.072 14.653  0.004  4.112   5.6388e-02
   3_adp:   0.979  0.007  0.072 14.653  0.004  4.112   5.6388e-02
   3_occ:   0.979  0.007  0.072 14.653  0.004  4.112   5.6388e-02
   4_bss:   0.979  0.007  0.072 14.653  0.004  4.112   5.6388e-02
   4_xyz:   0.985  0.007  0.076 14.499  0.004  4.116   5.6793e-02
   4_adp:   0.985  0.007  0.076 14.499  0.004  4.116   5.6793e-02
   4_occ:   0.985  0.007  0.076 14.499  0.004  4.116   5.6793e-02
   5_bss:   0.985  0.007  0.076 14.499  0.004  4.116   5.6793e-02
   5_xyz:   0.983  0.007  0.075 14.466  0.004  4.112   5.7153e-02
   5_adp:   0.983  0.007  0.075 14.466  0.004  4.112   5.7153e-02
   5_occ:   0.983  0.007  0.075 14.466  0.004  4.112   5.7153e-02
   5_bss:   0.983  0.007  0.075 14.466  0.004  4.112   5.7153e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.273   2.4279e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.273   2.4279e-01
   1_xyz:   9.514  0.049  0.317 82.986  0.039  2.205   8.9222e-02
   1_adp:   9.514  0.049  0.317 82.986  0.039  2.205   8.9222e-02
   1_occ:   9.514  0.049  0.317 82.986  0.039  2.205   8.9222e-02
   2_bss:   9.514  0.049  0.317 82.986  0.039  2.205   8.9222e-02
   2_xyz:   7.200  0.054  0.280 83.542  0.036  2.254   1.0707e-01
   2_adp:   7.200  0.054  0.280 83.542  0.036  2.254   1.0707e-01
   2_occ:   7.200  0.054  0.280 83.542  0.036  2.254   1.0707e-01
   3_bss:   7.200  0.054  0.280 83.542  0.036  2.254   1.0707e-01
   3_xyz:   6.911  0.040  0.236 82.367  0.035  2.252   3.6338e-02
   3_adp:   6.911  0.040  0.236 82.367  0.035  2.252   3.6338e-02
   3_occ:   6.911  0.040  0.236 82.367  0.035  2.252   3.6338e-02
   4_bss:   6.911  0.040  0.236 82.367  0.035  2.252   3.6338e-02
   4_xyz:   6.903  0.042  0.257 82.609  0.032  2.354   3.8402e-02
   4_adp:   6.903  0.042  0.257 82.609  0.032  2.354   3.8402e-02
   4_occ:   6.903  0.042  0.257 82.609  0.032  2.354   3.8402e-02
   5_bss:   6.903  0.042  0.257 82.609  0.032  2.354   3.8402e-02
   5_xyz:   6.978  0.050  0.248 82.599  0.034  2.374   3.8227e-02
   5_adp:   6.978  0.050  0.248 82.599  0.034  2.374   3.8227e-02
   5_occ:   6.978  0.050  0.248 82.599  0.034  2.374   3.8227e-02
   5_bss:   6.978  0.050  0.248 82.599  0.034  2.374   3.8227e-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:  98.44   0.00  16.97  98.44   0.00  13.19  65.08   4.34  37.57
   1_occ:  98.44   0.00  16.97  98.44   0.00  13.19  65.08   4.34  37.57
   2_bss:  98.44   0.00  16.97  98.44   0.00  13.19  65.08   4.34  37.57
   2_xyz:  98.44   0.00  16.97  98.44   0.00  13.19  65.08   4.34  37.57
   2_adp:  76.92   0.00  17.55  76.92   0.00  13.16  75.74   5.47  41.45
   2_occ:  76.92   0.00  17.55  76.92   0.00  13.16  75.74   5.47  41.45
   3_bss:  76.92   0.00  17.55  76.92   0.00  13.16  75.74   5.47  41.45
   3_xyz:  76.92   0.00  17.55  76.92   0.00  13.16  75.74   5.47  41.45
   3_adp:  84.20   0.76  17.38  84.20   0.76  12.96  83.00   5.11  41.42
   3_occ:  84.20   0.76  17.38  84.20   0.76  12.96  83.00   5.11  41.42
   4_bss:  84.20   0.76  17.38  84.20   0.76  12.96  83.00   5.11  41.42
   4_xyz:  84.20   0.76  17.38  84.20   0.76  12.96  83.00   5.11  41.42
   4_adp:  90.11   0.00  17.17  88.49   0.70  12.78  90.11   0.00  41.10
   4_occ:  90.11   0.00  17.17  88.49   0.70  12.78  90.11   0.00  41.10
   5_bss:  90.11   0.00  17.17  88.49   0.70  12.78  90.11   0.00  41.10
   5_xyz:  90.11   0.00  17.17  88.49   0.70  12.78  90.11   0.00  41.10
   5_adp:  90.37   0.00  16.84  89.49   0.76  12.56  90.37   0.00  40.18
   5_occ:  90.37   0.00  16.84  89.49   0.76  12.56  90.37   0.00  40.18
   5_bss:  90.38   0.00  16.85  89.50   0.76  12.56  90.38   0.00  40.18
------------------------------------------------------------------------
 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:    1.984    0.011    0.308
   1_adp:    1.984    0.011    0.308
   1_occ:    1.984    0.011    0.308
   2_bss:    1.984    0.011    0.308
   2_xyz:    1.591    0.038    0.483
   2_adp:    1.591    0.038    0.483
   2_occ:    1.591    0.038    0.483
   3_bss:    1.591    0.038    0.483
   3_xyz:    1.544    0.049    0.531
   3_adp:    1.544    0.049    0.531
   3_occ:    1.544    0.049    0.531
   4_bss:    1.544    0.049    0.531
   4_xyz:    1.431    0.060    0.556
   4_adp:    1.431    0.060    0.556
   4_occ:    1.431    0.060    0.556
   5_bss:    1.431    0.060    0.556
   5_xyz:    1.363    0.061    0.567
   5_adp:    1.363    0.061    0.567
   5_occ:    1.363    0.061    0.567
   5_bss:    1.363    0.061    0.567
------------------------------------------------------------------------

CPU time actual refinement: 335.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/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_196/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_196/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.93 
  Macro-tasks:
    bulk solvent and scale       = 37.25  
    individual site refinement   = 143.39 
    weights calculation          = 29.25  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 216.55 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 107.88 
    alpha_beta                      = 8.42   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.06 
    fmodel                         = 6.32   
    r_factors                      = 0.19   
    phase_errors                   = 10.58  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.72 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.733 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    639 calls, 107.61 s
gradients_fft:          584 calls, 104.28 s

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

# Date 2008-01-16 Time 04:14:55 PST -0800 (1200485695.42 s)
Start R-work = 0.4090, R-free = 0.4069 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1775 (no bulk solvent and anisotropic scale)

Start R-work = 0.3989, R-free = 0.3962
Final R-work = 0.1133, R-free = 0.1596