# Date 2008-01-16 Time 01:44:52 PST -0800 (1200476692.34 s)
#phil __OFF__

Command line arguments: "../540.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4581
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 540

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 84.6622, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96122
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951939

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96122
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951939

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1966 [2152/2180]  1940   212   9.9%
  bin  2:  4.1966 -  3.3434 [2068/2087]  1858   210  10.2%
  bin  3:  3.3434 -  2.9245 [2045/2065]  1841   204  10.0%
  bin  4:  2.9245 -  2.6587 [2033/2058]  1835   198   9.7%
  bin  5:  2.6587 -  2.4691 [2011/2030]  1806   205  10.2%
  bin  6:  2.4691 -  2.3241 [2001/2048]  1801   200  10.0%
  bin  7:  2.3241 -  2.2081 [1976/2008]  1776   200  10.1%
  bin  8:  2.2081 -  2.1123 [1988/2024]  1789   199  10.0%
  bin  9:  2.1123 -  2.0311 [1991/2020]  1795   196   9.8%
  bin 10:  2.0311 -  1.9612 [1324/1994]  1189   135  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/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:
        1.77 -     2.40: 33
        2.40 -     3.02: 2104
        3.02 -     3.65: 4716
        3.65 -     4.27: 9164
        4.27 -     4.90: 12642
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.773 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.833 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.890 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28654 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_540/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 84.6622 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4496   r_free= 0.4530   ksol= 0.00   Bsol= 0.00   scale= 0.820    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.247475                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.3742 0.3586      6.5476      6.5225|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.3608 0.3560      6.7018      6.7126|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.3994 0.3924       6.609      6.6812|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.4165 0.4486      6.4634      6.4395|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.4597 0.4852      6.3456      6.3643|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.4754 0.5132      6.2364      6.2161|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.4944 0.4602      6.2407       6.154|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.4976 0.4983      6.1522       6.149|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.4959 0.4865      6.1021      6.0971|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.5127 0.5279      6.0988      6.1097|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.5215 0.5015      6.0348      6.0349|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.4928 0.5361      5.9587      5.9881|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.5138 0.5188      5.8752      5.8374|
| 14:  2.0102 -  1.9612 0.55    695   80 0.5325 0.5198      5.8278      5.7471|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6806  1394   154  0.71  33.55   0.82     0.73      66916.19|
|  2:  4.6806 -  3.7346  1359   148  0.73  32.41   0.91     0.80      90783.03|
|  3:  3.7346 -  3.2682  1310   153  0.65  40.02   0.87     0.77      97007.18|
|  4:  3.2682 -  2.9720  1326   143  0.57  46.02   0.84     0.67      87500.59|
|  5:  2.9720 -  2.7605  1303   145  0.48  53.46   0.77     0.57      75133.17|
|  6:  2.7605 -  2.5986  1286   144  0.45  55.96   0.75     0.53      64878.07|
|  7:  2.5986 -  2.4691  1302   142  0.46  55.46   0.75     0.52      57769.18|
|  8:  2.4691 -  2.3621  1273   146  0.45  56.41   0.75     0.52      52045.79|
|  9:  2.3621 -  2.2715  1299   143  0.45  56.21   0.76     0.52      46633.68|
| 10:  2.2715 -  2.1933  1272   136  0.43  57.31   0.77     0.52      43611.33|
| 11:  2.1933 -  2.1249  1271   146  0.41  59.40   0.78     0.50      41231.22|
| 12:  2.1249 -  2.0644  1273   139  0.37  62.48   0.78     0.46      41562.26|
| 13:  2.0644 -  2.0102  1267   140  0.32  65.97   0.76     0.40      36661.91|
| 14:  2.0102 -  1.9612   695    80  0.32  65.78   0.72     0.37      29753.16|
|alpha:            min =        0.37 max =            0.80 mean =         0.57|
|beta:             min =    29753.16 max =        97007.18 mean =     60751.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.19|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.64|
|-----------------------------------------------------------------------------|

============================== 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 = 9.977218              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.252   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.891901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.836   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      712 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1537 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2665 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3989 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5115 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6619 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7811 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.251 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.924 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4582   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.252324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4412   r_free= 0.4416   ksol= 0.35   Bsol= 9.31   scale= 1.019    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.09,7.91,9.76,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.243547                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.700131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.117   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.847489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.733   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4412      final r-factor (work) = 0.3506          |
| start r-factor (free) = 0.4416      final r-factor (free) = 0.3741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.4498 = 8.70 * 0.50 * 6.2525 + 1.00 * 53.2509                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8022 = 8.70 * 0.50 * 6.1324 + 1.00 * 0.1259                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3506      final r-factor (work) = 0.2946          |
| start r-factor (free) = 0.3741      final r-factor (free) = 0.3397          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2114 = 0.85 * 1.00 * 6.1324 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1012 = 0.85 * 1.00 * 6.0031 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.10   11.31    None  None   None       |
|    all(noH): 2823   0      0.00    57.10   11.31    None  None   None       |
|    Sol.    : 438    0      0.00    56.55   26.02    None  None   None       |
|    Mac.    : 2385   0      0.00    57.10   8.61     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 -   5.710: 1075   |   5:    28.548 -  34.258:  111        |
|      1:     5.710 -  11.419:  738   |   6:    34.258 -  39.967:   92        |
|      2:    11.419 -  17.129:  372   |   7:    39.967 -  45.677:   29        |
|      3:    17.129 -  22.838:  239   |   8:    45.677 -  51.386:   23        |
|      4:    22.838 -  28.548:  139   |   9:    51.386 -  57.096:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2946 r_free = 0.3397             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2943 r_free = 0.3402             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2943   r_free= 0.3402   ksol= 0.35   Bsol= 9.31   scale= 1.099    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.09,7.91,9.76,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.967789                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2898   r_free= 0.3355   ksol= 0.32   Bsol= 20.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.12,6.56,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.966022                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.812130              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.394868              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.760  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2898      final r-factor (work) = 0.2118          |
| start r-factor (free) = 0.3355      final r-factor (free) = 0.2619          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5701 = 3.81 * 0.50 * 6.0041 + 1.00 * 0.1259                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1668 = 3.81 * 0.50 * 5.8262 + 1.00 * 0.0617                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2118      final r-factor (work) = 0.1928          |
| start r-factor (free) = 0.2619      final r-factor (free) = 0.2406          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3333 = 0.39 * 1.00 * 5.8262 + 1.00 * 0.0327                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2431 = 0.39 * 1.00 * 5.6483 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.40   11.71    None  None   None       |
|    all(noH): 2823   0      0.00    64.40   11.71    None  None   None       |
|    Sol.    : 438    0      1.49    61.78   31.02    None  None   None       |
|    Mac.    : 2385   0      0.00    64.40   8.16     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 -   6.440: 1285   |   5:    32.200 -  38.639:  130        |
|      1:     6.440 -  12.880:  757   |   6:    38.639 -  45.079:   90        |
|      2:    12.880 -  19.320:  257   |   7:    45.079 -  51.519:   42        |
|      3:    19.320 -  25.760:  123   |   8:    51.519 -  57.959:   18        |
|      4:    25.760 -  32.200:  117   |   9:    57.959 -  64.399:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1928 r_free = 0.2406             target_work(ml) = 5.610         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1925 r_free = 0.2405             target_work(ml) = 5.610         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1925   r_free= 0.2405   ksol= 0.32   Bsol= 20.00   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,4.12,6.56,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.609575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1908   r_free= 0.2394   ksol= 0.32   Bsol= 33.32   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.93,4.16,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.607108                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.735054              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.067  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.979972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.639  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1908      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2394      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7957 = 2.74 * 0.50 * 5.6554 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5592 = 2.74 * 0.50 * 5.4838 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1876      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3847 = 0.98 * 1.00 * 5.4838 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2121 = 0.98 * 1.00 * 5.3058 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.50   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    76.50   12.44    None  None   None       |
|    Sol.    : 438    0      2.38    72.32   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    76.50   8.12     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 -   7.650: 1549   |   5:    38.251 -  45.902:  108        |
|      1:     7.650 -  15.301:  633   |   6:    45.902 -  53.552:   71        |
|      2:    15.301 -  22.951:  180   |   7:    53.552 -  61.202:   50        |
|      3:    22.951 -  30.601:   95   |   8:    61.202 -  68.853:   17        |
|      4:    30.601 -  38.251:  114   |   9:    68.853 -  76.503:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1778             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1314 r_free = 0.1777             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1777   ksol= 0.32   Bsol= 33.32   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.93,4.16,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.277367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1317   r_free= 0.1766   ksol= 0.31   Bsol= 33.32   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.78,3.46,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275510                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.761366              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.899  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700652              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1766      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7330 = 1.76 * 0.50 * 5.3062 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6690 = 1.76 * 0.50 * 5.2388 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6832 = 0.70 * 1.00 * 5.2388 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6513 = 0.70 * 1.00 * 5.1922 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.86   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    83.86   12.44    None  None   None       |
|    Sol.    : 438    0      1.66    77.19   36.04    None  None   None       |
|    Mac.    : 2385   0      0.00    83.86   8.11     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 -   8.386: 1678   |   5:    41.928 -  50.313:  101        |
|      1:     8.386 -  16.771:  569   |   6:    50.313 -  58.699:   52        |
|      2:    16.771 -  25.157:  158   |   7:    58.699 -  67.085:   35        |
|      3:    25.157 -  33.542:  103   |   8:    67.085 -  75.470:   11        |
|      4:    33.542 -  41.928:  111   |   9:    75.470 -  83.856:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1621             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1620             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1620   ksol= 0.31   Bsol= 33.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.78,3.46,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1619   ksol= 0.32   Bsol= 35.20   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.78,3.46,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184847                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.262877              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.842475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.233  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5256 = 3.26 * 0.50 * 5.1919 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4782 = 3.26 * 0.50 * 5.1534 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3582 = 0.84 * 1.00 * 5.1534 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3572 = 0.84 * 1.00 * 5.1368 + 1.00 * 0.0295                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.76   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    84.76   12.33    None  None   None       |
|    Sol.    : 438    0      1.11    77.39   35.82    None  None   None       |
|    Mac.    : 2385   0      0.00    84.76   8.02     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 -   8.476: 1706   |   5:    42.382 -  50.858:   94        |
|      1:     8.476 -  16.953:  546   |   6:    50.858 -  59.334:   54        |
|      2:    16.953 -  25.429:  152   |   7:    59.334 -  67.811:   32        |
|      3:    25.429 -  33.905:  112   |   8:    67.811 -  76.287:   10        |
|      4:    33.905 -  42.382:  111   |   9:    76.287 -  84.763:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1584             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1583             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1583   ksol= 0.32   Bsol= 35.20   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.78,3.46,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.0969 0.1306      5.3725      5.5347|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.0824 0.1120      5.4054      5.6229|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.1019 0.1503      5.4444      5.8193|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.1180 0.1587      5.4324      5.6174|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.1228 0.1623      5.2914      5.4671|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.1194 0.1886      5.1957      5.4724|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.1202 0.1661      5.1498      5.3778|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.1130 0.1713      5.0712      5.3279|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.1153 0.1831       5.035      5.3249|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.1105 0.1818      4.9693      5.2487|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.1120 0.1764      4.9343        5.29|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.1068 0.1669      4.8562      5.1027|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.1148 0.1827      4.7949      5.0718|
| 14:  2.0102 -  1.9612 0.55    695   80 0.1061 0.1642      4.6917      4.9035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6806  1394   154  0.94   8.99   0.99     0.97       7209.09|
|  2:  4.6806 -  3.7346  1359   148  0.96   7.68   1.03     1.01       8633.70|
|  3:  3.7346 -  3.2682  1310   153  0.93  11.19   1.04     1.03      10028.62|
|  4:  3.2682 -  2.9720  1326   143  0.92  13.57   1.02     1.00      10129.23|
|  5:  2.9720 -  2.7605  1303   145  0.90  15.68   1.00     0.97       7924.95|
|  6:  2.7605 -  2.5986  1286   144  0.90  15.94   0.99     0.96       7070.33|
|  7:  2.5986 -  2.4691  1302   142  0.91  15.21   0.99     0.96       6119.85|
|  8:  2.4691 -  2.3621  1273   146  0.90  15.91   1.00     0.97       5651.78|
|  9:  2.3621 -  2.2715  1299   143  0.91  15.74   1.01     0.99       5182.38|
| 10:  2.2715 -  2.1933  1272   136  0.90  16.17   1.01     0.98       4683.37|
| 11:  2.1933 -  2.1249  1271   146  0.90  16.48   1.01     0.98       4406.67|
| 12:  2.1249 -  2.0644  1273   139  0.91  15.06   1.01     0.99       3884.94|
| 13:  2.0644 -  2.0102  1267   140  0.90  16.51   1.01     1.01       3440.40|
| 14:  2.0102 -  1.9612   695    80  0.90  15.75   1.00     0.97       2751.30|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2751.30 max =        10129.23 mean =      6377.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.16|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1583   ksol= 0.32   Bsol= 39.92   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.03,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136426                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1583   ksol= 0.32   Bsol= 39.92   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.03,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136426                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6806 0.99   1394  154 0.0969 0.1308      5.3734      5.5362|
|  2:  4.6806 -  3.7346 0.99   1359  148 0.0826 0.1121      5.4067      5.6244|
|  3:  3.7346 -  3.2682 0.99   1310  153 0.1020 0.1504      5.4451      5.8198|
|  4:  3.2682 -  2.9720 0.99   1326  143 0.1181 0.1586      5.4324      5.6175|
|  5:  2.9720 -  2.7605 0.99   1303  145 0.1226 0.1620      5.2909      5.4656|
|  6:  2.7605 -  2.5986 0.98   1286  144 0.1193 0.1888      5.1952      5.4732|
|  7:  2.5986 -  2.4691 0.99   1302  142 0.1201 0.1659      5.1496      5.3775|
|  8:  2.4691 -  2.3621 0.98   1273  146 0.1130 0.1711      5.0707      5.3272|
|  9:  2.3621 -  2.2715 0.98   1299  143 0.1153 0.1832      5.0348      5.3257|
| 10:  2.2715 -  2.1933 0.98   1272  136 0.1105 0.1819      4.9687      5.2468|
| 11:  2.1933 -  2.1249 0.99   1271  146 0.1118 0.1762      4.9338      5.2894|
| 12:  2.1249 -  2.0644 0.98   1273  139 0.1068 0.1667       4.855      5.1013|
| 13:  2.0644 -  2.0102 0.97   1267  140 0.1146 0.1822      4.7938      5.0692|
| 14:  2.0102 -  1.9612 0.55    695   80 0.1062 0.1642      4.6911      4.9052|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6806  1394   154  0.94   9.01   0.99     0.97       7231.22|
|  2:  4.6806 -  3.7346  1359   148  0.96   7.69   1.03     1.01       8655.13|
|  3:  3.7346 -  3.2682  1310   153  0.93  11.20   1.04     1.03      10046.24|
|  4:  3.2682 -  2.9720  1326   143  0.92  13.57   1.02     1.00      10128.93|
|  5:  2.9720 -  2.7605  1303   145  0.90  15.68   1.00     0.97       7926.50|
|  6:  2.7605 -  2.5986  1286   144  0.90  15.94   0.99     0.96       7067.78|
|  7:  2.5986 -  2.4691  1302   142  0.91  15.21   1.00     0.96       6118.24|
|  8:  2.4691 -  2.3621  1273   146  0.90  15.90   1.00     0.97       5643.40|
|  9:  2.3621 -  2.2715  1299   143  0.91  15.73   1.02     0.99       5178.33|
| 10:  2.2715 -  2.1933  1272   136  0.90  16.16   1.01     0.98       4677.79|
| 11:  2.1933 -  2.1249  1271   146  0.90  16.47   1.01     0.98       4401.40|
| 12:  2.1249 -  2.0644  1273   139  0.91  15.03   1.01     0.99       3872.52|
| 13:  2.0644 -  2.0102  1267   140  0.90  16.48   1.02     1.01       3430.35|
| 14:  2.0102 -  1.9612   695    80  0.90  15.73   1.00     0.97       2746.43|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2746.43 max =        10128.93 mean =      6378.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.15|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.619)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.91    87.67   15.24    None  None   None       |
|    all(noH): 2823   0      2.91    87.67   15.24    None  None   None       |
|    Sol.    : 438    0      4.01    80.30   38.73    None  None   None       |
|    Mac.    : 2385   0      2.91    87.67   10.93    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:     2.906 -  11.382: 1706   |   5:    45.287 -  53.764:   94        |
|      1:    11.382 -  19.859:  546   |   6:    53.764 -  62.240:   54        |
|      2:    19.859 -  28.335:  152   |   7:    62.240 -  70.716:   32        |
|      3:    28.335 -  36.811:  112   |   8:    70.716 -  79.193:   10        |
|      4:    36.811 -  45.287:  111   |   9:    79.193 -  87.669:    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)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.364 - 5.711
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 299
   mapped sites are within: 0.738 - 5.711

peak=   11.086 closest distance to " CB  VAL A 230 " =    1.447
peak=    8.041 closest distance to " CG2 VAL A 296 " =    1.172
peak=    6.150 closest distance to " CG  LEU A   5 " =    1.188
peak=    5.751 closest distance to " O   HOH Z 278 " =    1.163
peak=    5.506 closest distance to " NE2 GLN A  11 " =    1.107
peak=    5.329 closest distance to " CD2 LEU A   5 " =    1.202
peak=    5.275 closest distance to " O   HOH Z 193 " =    1.648
peak=    5.223 closest distance to " NH2 ARG A  56 " =    2.115
peak=    5.127 closest distance to " CB  VAL A 296 " =    1.056
peak=    5.059 closest distance to " O   HOH Z 126 " =    1.952
peak=    5.056 closest distance to " O   HOH Z 124 " =    1.481
peak=    5.056 closest distance to " O   HOH Z 142 " =    1.767
peak=    5.052 closest distance to " CG  LEU A 228 " =    1.198
peak=    5.019 closest distance to " CB  GLN A 183 " =    1.293
peak=    4.916 closest distance to " CB  SER A  63 " =    1.253
peak=    4.909 closest distance to " CG  PRO A  54 " =    1.141
peak=    4.883 closest distance to " CB  GLN A 223 " =    1.487
peak=    4.823 closest distance to " O   HOH Z 232 " =    2.302
peak=    4.721 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.570 closest distance to " O   HOH Z 316 " =    2.865
peak=    4.565 closest distance to " O   HOH Z 427 " =    2.826
peak=    4.530 closest distance to " O   HOH Z 368 " =    2.139
peak=    4.508 closest distance to " CB  VAL A 230 " =    1.174
peak=    4.455 closest distance to " O   SER A  87 " =    2.291
peak=    4.454 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.453 closest distance to " OD1 ASN A  69 " =    2.637
peak=    4.406 closest distance to " O   HOH Z 132 " =    0.929
peak=    4.402 closest distance to " O   HOH Z 202 " =    1.085
peak=    4.361 closest distance to " CB  ASN A 148 " =    1.443
peak=    4.347 closest distance to " CB  PRO A  54 " =    0.901
peak=    4.345 closest distance to " O   HOH Z 128 " =    2.013
peak=    4.344 closest distance to " O   HOH Z 203 " =    1.613
peak=    4.334 closest distance to " O   PRO A 198 " =    1.537
peak=    4.321 closest distance to " CB  SER A   3 " =    1.341
peak=    4.304 closest distance to " O   HOH Z 411 " =    3.763
peak=    4.293 closest distance to " CB  TRP A 179 " =    1.286
peak=    4.289 closest distance to " O   HOH Z 234 " =    3.707
peak=    4.288 closest distance to " CB  TYR A 169 " =    0.918
peak=    4.287 closest distance to " O   HOH Z 280 " =    2.958
peak=    4.268 closest distance to " O   HOH Z  93 " =    2.471
peak=    4.239 closest distance to " O   HOH Z  78 " =    1.811
peak=    4.236 closest distance to " O   HOH Z 303 " =    2.012
peak=    4.228 closest distance to " O   HOH Z 263 " =    1.475
peak=    4.209 closest distance to " O   HOH Z 298 " =    1.838
peak=    4.204 closest distance to " CA  VAL A  41 " =    0.784
peak=    4.174 closest distance to " CA  ALA A  21 " =    1.102
peak=    4.171 closest distance to " CB  GLU A 152 " =    1.164
peak=    4.169 closest distance to " O   HOH Z 403 " =    1.714
peak=    4.168 closest distance to " O   HOH Z  48 " =    1.579
peak=    4.145 closest distance to " O   HOH Z 371 " =    3.212
peak=    4.080 closest distance to " O   HOH Z 236 " =    1.829
peak=    4.080 closest distance to " CD1AILE A 234 " =    0.868
peak=    4.072 closest distance to " O   HOH Z 260 " =    1.210
peak=    4.066 closest distance to " CD2 LEU A 228 " =    1.149
peak=    4.065 closest distance to " O   HOH Z 346 " =    1.497
peak=    4.058 closest distance to " O   HOH Z  97 " =    1.935
peak=    4.046 closest distance to " CG  PRO A 213 " =    1.192
peak=    4.030 closest distance to " O   HOH Z   9 " =    2.311
peak=    4.020 closest distance to " CG1BVAL A  72 " =    1.497
peak=    4.010 closest distance to " O   HOH Z 369 " =    1.928
peak=    3.961 closest distance to " OG BSER A 164 " =    2.165
peak=    3.946 closest distance to " O   HOH Z  59 " =    2.070
peak=    3.944 closest distance to " CB  GLU A 128 " =    1.119
peak=    3.935 closest distance to " O   HOH Z 426 " =    1.480
peak=    3.933 closest distance to " O   HOH Z  61 " =    1.612
peak=    3.921 closest distance to " O   HOH Z 345 " =    3.121
peak=    3.908 closest distance to " O   HOH Z  54 " =    1.562
peak=    3.894 closest distance to " CB  GLU A 277 " =    3.504
peak=    3.887 closest distance to " O   HOH Z 108 " =    1.134
peak=    3.871 closest distance to " O   HOH Z 130 " =    2.346
peak=    3.869 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.868 closest distance to " CG  ARG A  66 " =    2.748
peak=    3.864 closest distance to " CA  TYR A  30 " =    1.019
peak=    3.864 closest distance to " O   HOH Z 392 " =    3.059
peak=    3.863 closest distance to " O   HOH Z 344 " =    2.670
peak=    3.845 closest distance to " O   HOH Z 214 " =    2.318
peak=    3.844 closest distance to " O   HOH Z 425 " =    2.083
peak=    3.843 closest distance to " O   HOH Z 423 " =    1.843
peak=    3.838 closest distance to " OD2 ASP A 286 " =    2.676
peak=    3.837 closest distance to " CB  VAL A 202 " =    1.661
peak=    3.833 closest distance to " O   HOH Z  85 " =    1.338
peak=    3.831 closest distance to " ND2 ASN A 187 " =    1.574
peak=    3.811 closest distance to " OE1 GLU A   2 " =    2.145
peak=    3.802 closest distance to " O   HOH Z 193 " =    2.027
peak=    3.783 closest distance to " O   HOH Z  44 " =    1.835
peak=    3.776 closest distance to " O   HOH Z 134 " =    1.398
peak=    3.775 closest distance to " NE2 GLN A  58 " =    4.189
peak=    3.761 closest distance to " CB  VAL A 265 " =    1.247
peak=    3.759 closest distance to " CB  ARG A  79 " =    1.450
peak=    3.746 closest distance to " O   HOH Z 425 " =    1.326
peak=    3.745 closest distance to " O   HOH Z 192 " =    1.551
peak=    3.692 closest distance to " CD2 TRP A 179 " =    1.394
peak=    3.686 closest distance to " NZ  LYS A 117 " =    3.094
peak=    3.684 closest distance to " O   HOH Z 344 " =    1.361
peak=    3.683 closest distance to " O   HOH Z 261 " =    2.169
peak=    3.672 closest distance to " O   HOH Z 273 " =    2.737
peak=    3.661 closest distance to " O   HOH Z 112 " =    1.605
peak=    3.661 closest distance to " O   HOH Z 374 " =    2.446
peak=    3.652 closest distance to " CB  TRP A 266 " =    1.004
peak=    3.638 closest distance to " O   HOH Z 189 " =    2.571
peak=    3.638 closest distance to " O   HOH Z 236 " =    1.515
peak=    3.633 closest distance to " O   HOH Z 322 " =    2.056
peak=    3.631 closest distance to " CB  ARG A 139 " =    0.969
peak=    3.626 closest distance to " CA  ARG A 275 " =    1.901
peak=    3.620 closest distance to " CG2 ILE A  20 " =    1.537
peak=    3.619 closest distance to " O   MET A 105 " =    1.815
peak=    3.614 closest distance to " O   HOH Z 158 " =    2.973
peak=    3.614 closest distance to " CA  VAL A 126 " =    1.003
peak=    3.607 closest distance to " O   HOH Z 329 " =    3.702
peak=    3.595 closest distance to " O   HOH Z 250 " =    1.282
peak=    3.595 closest distance to " CA  ALA A 248 " =    1.307
peak=    3.590 closest distance to " O   HOH Z  48 " =    1.376
peak=    3.588 closest distance to " CG1 ILE A  33 " =    1.350
peak=    3.588 closest distance to " CB  ASN A  39 " =    0.863
peak=    3.585 closest distance to " O   HOH Z 402 " =    1.379
peak=    3.584 closest distance to " CB BVAL A  41 " =    1.336
peak=    3.583 closest distance to " CA  THR A 221 " =    0.894
peak=    3.582 closest distance to " O   HOH Z 422 " =    2.630
peak=    3.573 closest distance to " CG  PRO A 198 " =    1.165
peak=    3.570 closest distance to " CD BLYS A 290 " =    1.172
peak=    3.566 closest distance to " O   HOH Z 180 " =    2.183
peak=    3.563 closest distance to " O   HOH Z 407 " =    2.534
peak=    3.559 closest distance to " CG2 ILE A 120 " =    1.269
peak=    3.549 closest distance to " O   HOH Z 172 " =    3.815
peak=    3.548 closest distance to " O   HOH Z   3 " =    1.620
peak=    3.546 closest distance to " CA  ASN A 215 " =    1.165
peak=    3.545 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.542 closest distance to " O   HOH Z 303 " =    1.680
peak=    3.536 closest distance to " CG  MET A 185 " =    1.111
peak=    3.534 closest distance to " O   HOH Z 389 " =    1.732
peak=    3.530 closest distance to " O   HOH Z 118 " =    1.362
peak=    3.528 closest distance to " O   HOH Z 334 " =    1.388
peak=    3.522 closest distance to " CA  ALA A  51 " =    0.997
peak=    3.520 closest distance to " O   HOH Z 128 " =    2.013
peak=    3.518 closest distance to " O   HOH Z 248 " =    1.777
peak=    3.516 closest distance to " O   HOH Z 284 " =    1.601
peak=    3.515 closest distance to " OG1 THR A 294 " =    2.336
peak=    3.514 closest distance to " O   HOH Z  10 " =    1.796
peak=    3.512 closest distance to " O   HOH Z 108 " =    2.128
peak=    3.511 closest distance to " O   HOH Z 227 " =    1.748
peak=    3.510 closest distance to " OG  SER A  22 " =    2.842
peak=    3.509 closest distance to " NE2 GLN A  58 " =    5.711
peak=    3.505 closest distance to " CB  SER A  26 " =    1.613
peak=    3.492 closest distance to " O   HOH Z 366 " =    2.850
peak=    3.486 closest distance to " CA  ASN A 176 " =    1.066
peak=    3.485 closest distance to " O   HOH Z 151 " =    1.687
peak=    3.479 closest distance to " O   HOH Z  88 " =    2.982
peak=    3.478 closest distance to " O   HOH Z 192 " =    1.140
peak=    3.476 closest distance to " CG2 THR A 221 " =    1.208
peak=    3.473 closest distance to " CB  LEU A 228 " =    1.417
peak=    3.473 closest distance to " O   HOH Z  80 " =    1.562
peak=    3.472 closest distance to " O   HOH Z  61 " =    1.581
peak=    3.471 closest distance to " O   HOH Z 280 " =    1.608
peak=    3.470 closest distance to " O   HOH Z  43 " =    2.159
peak=    3.464 closest distance to " CA  ALA A 291 " =    0.970
peak=    3.463 closest distance to " CE1 TYR A 186 " =    1.227
peak=    3.462 closest distance to " O   HOH Z 209 " =    2.460
peak=    3.460 closest distance to " O   HOH Z   9 " =    2.084
peak=    3.457 closest distance to " CD1 ILE A 106 " =    1.248
peak=    3.454 closest distance to " N   SER A 135 " =    1.359
peak=    3.449 closest distance to " O   HOH Z 247 " =    1.194
peak=    3.448 closest distance to " O   HOH Z 279 " =    2.124
peak=    3.446 closest distance to " O   HOH Z 145 " =    2.025
peak=    3.445 closest distance to " CB  ALA A 295 " =    1.298
peak=    3.444 closest distance to " O   HOH Z 213 " =    1.663
peak=    3.444 closest distance to " CG  MET A 185 " =    1.286
peak=    3.444 closest distance to " O   HOH Z 276 " =    1.213
peak=    3.436 closest distance to " CG  LEU A 167 " =    1.166
peak=    3.435 closest distance to " O   HOH Z 123 " =    1.008
peak=    3.433 closest distance to " O   HOH Z 227 " =    2.170
peak=    3.429 closest distance to " CG AARG A 275 " =    1.033
peak=    3.425 closest distance to " O   HOH Z 209 " =    2.244
peak=    3.417 closest distance to " O   HOH Z 245 " =    1.370
peak=    3.412 closest distance to " CB  LEU A 255 " =    0.738
peak=    3.411 closest distance to " O   HOH Z 151 " =    1.803
peak=    3.401 closest distance to " O   HOH Z 222 " =    2.391
peak=    3.401 closest distance to " CE2 TRP A 179 " =    1.625
peak=    3.400 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.397 closest distance to " O   HOH Z 406 " =    1.508
peak=    3.395 closest distance to " CA  ALA A 158 " =    1.209
peak=    3.393 closest distance to " O   HOH Z  59 " =    2.068
peak=    3.392 closest distance to " O   HOH Z 135 " =    1.862
peak=    3.390 closest distance to " O   HOH Z 133 " =    1.473
peak=    3.386 closest distance to " CB  ARG A 190 " =    1.753
peak=    3.386 closest distance to " N   ASN A  39 " =    1.224
peak=    3.376 closest distance to " CA  PHE A 283 " =    1.341
peak=    3.375 closest distance to " CB  THR A  31 " =    1.757
peak=    3.375 closest distance to " CD1 ILE A  33 " =    1.658
peak=    3.371 closest distance to " O   HOH Z 164 " =    2.075
peak=    3.369 closest distance to " O   HOH Z 173 " =    2.172
peak=    3.366 closest distance to " NH2 ARG A 156 " =    1.037
peak=    3.363 closest distance to " CB  ASP A 140 " =    0.881
peak=    3.360 closest distance to " CG  PRO A 243 " =    1.269
peak=    3.355 closest distance to " O   HOH Z 357 " =    1.910
peak=    3.352 closest distance to " O   HOH Z 327 " =    1.513
peak=    3.347 closest distance to " C   ALA A 299 " =    0.956
peak=    3.346 closest distance to " CD2 HIS A  81 " =    1.143
peak=    3.341 closest distance to " O   HOH Z 147 " =    1.626
peak=    3.338 closest distance to " CG BARG A 102 " =    1.848
peak=    3.337 closest distance to " O   ALA A   1 " =    1.738
peak=    3.331 closest distance to " CG  GLN A  77 " =    2.295
peak=    3.324 closest distance to " O   THR A  31 " =    1.536
peak=    3.322 closest distance to " CB  ALA A 248 " =    0.998
peak=    3.314 closest distance to " NH2 ARG A 219 " =    1.791
peak=    3.312 closest distance to " OD1 ASP A 231 " =    1.882
peak=    3.311 closest distance to " O   HOH Z  21 " =    1.769
peak=    3.301 closest distance to " OE1 GLN A  11 " =    1.685
peak=    3.295 closest distance to " O   HOH Z 265 " =    2.394
peak=    3.295 closest distance to " O   HOH Z 367 " =    3.425
peak=    3.295 closest distance to " O   HOH Z 261 " =    1.546
peak=    3.295 closest distance to " O   HOH Z  40 " =    1.397
peak=    3.293 closest distance to " O   HOH Z 189 " =    2.714
peak=    3.293 closest distance to " NH1 ARG A  14 " =    1.010
peak=    3.291 closest distance to " ND1 HIS A  81 " =    1.457
peak=    3.288 closest distance to " CG  MET A 188 " =    1.406
peak=    3.288 closest distance to " O   HOH Z 193 " =    1.518
peak=    3.286 closest distance to " O   HOH Z 423 " =    2.990
peak=    3.285 closest distance to " CA  THR A 264 " =    0.739
peak=    3.281 closest distance to " O   ALA A 158 " =    1.380
peak=    3.279 closest distance to " O   HOH Z 281 " =    4.468
peak=    3.279 closest distance to " CD2 LEU A 255 " =    1.275
peak=    3.278 closest distance to " CA  ARG A  36 " =    1.021
peak=    3.277 closest distance to " OD1 ASN A 148 " =    1.695
peak=    3.277 closest distance to " CD  LYS A 119 " =    1.506
peak=    3.274 closest distance to " CA  ALA A 295 " =    1.066
peak=    3.274 closest distance to " CG2 VAL A 257 " =    0.827
peak=    3.273 closest distance to " CD  ARG A 269 " =    1.047
peak=    3.272 closest distance to " O   HOH Z 419 " =    1.689
peak=    3.271 closest distance to " O   HOH Z 148 " =    3.228
peak=    3.268 closest distance to " O   HOH Z  80 " =    2.227
peak=    3.267 closest distance to " O   HOH Z 427 " =    3.045
peak=    3.264 closest distance to " CB  SER A 216 " =    0.821
peak=    3.256 closest distance to " CG  GLN A  58 " =    2.681
peak=    3.254 closest distance to " CD2 TYR A 186 " =    1.061
peak=    3.249 closest distance to " CZ2 TRP A 274 " =    1.630
peak=    3.245 closest distance to " O   HOH Z 352 " =    1.280
peak=    3.234 closest distance to " O   HOH Z 435 " =    2.074
peak=    3.232 closest distance to " O   HOH Z  63 " =    2.047
peak=    3.228 closest distance to " CB  VAL A 268 " =    0.878
peak=    3.227 closest distance to " CA  GLN A 194 " =    1.322
peak=    3.224 closest distance to " O   HOH Z 409 " =    3.519
peak=    3.224 closest distance to " CD2 TYR A  30 " =    0.917
peak=    3.223 closest distance to " O   HOH Z  49 " =    2.301
peak=    3.223 closest distance to " O   HOH Z 116 " =    1.711
peak=    3.223 closest distance to " OG BSER A 258 " =    3.300
peak=    3.221 closest distance to " CG2 THR A 294 " =    1.565
peak=    3.220 closest distance to " O   HOH Z  64 " =    2.008
peak=    3.220 closest distance to " O   SER A  26 " =    1.603
peak=    3.219 closest distance to " O   HOH Z 211 " =    2.431
peak=    3.217 closest distance to " O   HOH Z  43 " =    2.710
peak=    3.216 closest distance to " O   HOH Z 368 " =    3.633
peak=    3.214 closest distance to " O   HOH Z 411 " =    1.764
peak=    3.211 closest distance to " N   VAL A 126 " =    1.293
peak=    3.203 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.203 closest distance to " O   HOH Z 420 " =    1.786
peak=    3.202 closest distance to " CD  LYS A 166 " =    1.392
peak=    3.190 closest distance to " O   HOH Z 128 " =    1.961
peak=    3.185 closest distance to " O   GLY A  91 " =    1.686
peak=    3.178 closest distance to " CB  ASN A 215 " =    1.058
peak=    3.175 closest distance to " CB  ALA A   1 " =    1.213
peak=    3.172 closest distance to " O   HOH Z 175 " =    2.117
peak=    3.169 closest distance to " CA  ASP A 140 " =    1.142
peak=    3.166 closest distance to " OG  SER A  62 " =    2.972
peak=    3.165 closest distance to " O   HOH Z  68 " =    1.481
peak=    3.164 closest distance to " O   HOH Z 359 " =    1.853
peak=    3.164 closest distance to " CB  TRP A 150 " =    1.405
peak=    3.163 closest distance to " O   HOH Z 163 " =    1.947
peak=    3.163 closest distance to " O   HOH Z 171 " =    2.444
peak=    3.162 closest distance to " O   HOH Z 251 " =    1.524
peak=    3.161 closest distance to " O   HOH Z 438 " =    2.306
peak=    3.156 closest distance to " C   LYS A 290 " =    1.278
peak=    3.156 closest distance to " O   HOH Z 374 " =    2.998
peak=    3.155 closest distance to " CB  SER A  62 " =    1.287
peak=    3.150 closest distance to " CA  LEU A 282 " =    1.176
peak=    3.150 closest distance to " O   HOH Z 271 " =    1.898
peak=    3.150 closest distance to " O   HOH Z 102 " =    1.151
peak=    3.149 closest distance to " O   HOH Z 337 " =    3.709
peak=    3.142 closest distance to " O   HOH Z 163 " =    1.802
peak=    3.138 closest distance to " CD1 LEU A 228 " =    1.600
peak=    3.134 closest distance to " OD1 ASN A  45 " =    1.371
peak=    3.129 closest distance to " CB  GLN A 205 " =    1.330
peak=    3.126 closest distance to " CE  MET A  93 " =    1.456
peak=    3.126 closest distance to " O   HOH Z 250 " =    1.439
peak=    3.124 closest distance to " CB  ILE A  20 " =    1.466
peak=    3.110 closest distance to " CA  ASP A 191 " =    0.851
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.482
peak=    3.105 closest distance to " NH2BARG A 145 " =    2.069
peak=    3.101 closest distance to " CG2 VAL A  67 " =    1.010
peak=    3.098 closest distance to " O   HOH Z  40 " =    1.862
peak=    3.094 closest distance to " CB  ASN A 110 " =    1.229
peak=    3.087 closest distance to " O   HOH Z 353 " =    2.693
peak=    3.083 closest distance to " CB  TYR A  30 " =    1.536
peak=    3.080 closest distance to " O   HOH Z  63 " =    2.313
peak=    3.076 closest distance to " O   HOH Z 152 " =    1.531
peak=    3.060 closest distance to " O   HOH Z 383 " =    2.128
peak=    3.059 closest distance to " O   HOH Z  50 " =    1.492

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.232
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.811 - 5.232

peak=   -5.027 closest distance to " CG2 VAL A 230 " =    0.811
peak=   -4.664 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.471 closest distance to " CB  ALA A 161 " =    2.526
peak=   -4.444 closest distance to " O   HOH Z 266 " =    4.490
peak=   -4.330 closest distance to " SG  CYS A 254 " =    3.133
peak=   -4.212 closest distance to " O   VAL A  67 " =    2.681
peak=   -4.199 closest distance to " O   HOH Z 231 " =    1.789
peak=   -4.154 closest distance to " OXT GLY A 302 " =    2.752
peak=   -4.146 closest distance to " O   PRO A 163 " =    2.097
peak=   -4.047 closest distance to " O   HOH Z 166 " =    1.494
peak=   -4.040 closest distance to " N   GLN A  58 " =    1.678
peak=   -4.009 closest distance to " OG BSER A 134 " =    1.243
peak=   -4.006 closest distance to " CG2 VAL A 296 " =    1.460
peak=   -4.005 closest distance to " OD1 ASN A  39 " =    2.215
peak=   -3.997 closest distance to " C   HIS A 108 " =    1.198
peak=   -3.970 closest distance to " CD  GLN A  88 " =    2.267
peak=   -3.968 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -3.957 closest distance to " CG  GLN A 223 " =    2.223
peak=   -3.888 closest distance to " CB  ALA A 248 " =    1.935
peak=   -3.886 closest distance to " O   HOH Z 290 " =    1.039
peak=   -3.872 closest distance to " N   SER A 276 " =    1.294
peak=   -3.872 closest distance to " CD1 LEU A 101 " =    2.444
peak=   -3.871 closest distance to " CD2 LEU A 300 " =    2.899
peak=   -3.849 closest distance to " O   HOH Z  43 " =    1.787
peak=   -3.845 closest distance to " O   HOH Z  11 " =    1.880
peak=   -3.810 closest distance to " C   ALA A 158 " =    1.247
peak=   -3.796 closest distance to " CB  PRO A 280 " =    2.120
peak=   -3.768 closest distance to " CD1 LEU A 255 " =    2.730
peak=   -3.757 closest distance to " C   ASN A 187 " =    1.874
peak=   -3.737 closest distance to " O   MET A  40 " =    2.611
peak=   -3.737 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.736 closest distance to " O   ALA A 161 " =    1.665
peak=   -3.729 closest distance to " O   HOH Z  13 " =    1.451
peak=   -3.728 closest distance to " OG ASER A 134 " =    1.254
peak=   -3.726 closest distance to " OG  SER A  97 " =    2.166
peak=   -3.710 closest distance to " CB  PRO A 243 " =    2.577
peak=   -3.705 closest distance to " ND2 ASN A  45 " =    1.048
peak=   -3.698 closest distance to " O   VAL A  67 " =    2.749
peak=   -3.697 closest distance to " OG BSER A 134 " =    1.623
peak=   -3.688 closest distance to " C   GLN A 205 " =    1.987
peak=   -3.679 closest distance to " CG  GLU A   2 " =    1.989
peak=   -3.677 closest distance to " O   HOH Z 103 " =    1.820
peak=   -3.672 closest distance to " O   HOH Z  98 " =    1.977
peak=   -3.669 closest distance to " O   HOH Z 165 " =    2.025
peak=   -3.664 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.663 closest distance to " N   ALA A 226 " =    1.978
peak=   -3.648 closest distance to " CG  ASP A  50 " =    2.465
peak=   -3.641 closest distance to " O   HOH Z 198 " =    2.311
peak=   -3.640 closest distance to " CG  LYS A 193 " =    2.218
peak=   -3.637 closest distance to " CD  ARG A 139 " =    1.694
peak=   -3.612 closest distance to " CA  ASP A 298 " =    1.035
peak=   -3.609 closest distance to " N   ALA A 248 " =    1.620
peak=   -3.607 closest distance to " NH2AARG A 275 " =    5.088
peak=   -3.602 closest distance to " CG  PHE A 283 " =    2.667
peak=   -3.602 closest distance to " OG  SER A  62 " =    1.526
peak=   -3.595 closest distance to " O   HOH Z 166 " =    1.899
peak=   -3.593 closest distance to " N   THR A 157 " =    1.480
peak=   -3.592 closest distance to " N   HIS A 115 " =    1.831
peak=   -3.587 closest distance to " CE  MET A 105 " =    2.036
peak=   -3.585 closest distance to " O   HOH Z 407 " =    3.189
peak=   -3.582 closest distance to " CZ  TYR A 169 " =    1.723
peak=   -3.582 closest distance to " O   HOH Z 423 " =    2.144
peak=   -3.569 closest distance to " CE2 PHE A 218 " =    2.620
peak=   -3.569 closest distance to " O   HOH Z  97 " =    1.641
peak=   -3.566 closest distance to " CZ  PHE A  59 " =    1.543
peak=   -3.563 closest distance to " CB  ALA A 291 " =    2.417
peak=   -3.553 closest distance to " CB  ASN A  39 " =    2.086
peak=   -3.551 closest distance to " O   HOH Z 436 " =    1.497
peak=   -3.550 closest distance to " OXT GLY A 302 " =    3.506
peak=   -3.549 closest distance to " CG  LEU A 228 " =    1.048
peak=   -3.534 closest distance to " O   HOH Z 102 " =    1.717
peak=   -3.531 closest distance to " N   ALA A  43 " =    2.433
peak=   -3.530 closest distance to " O   ALA A   8 " =    1.855
peak=   -3.522 closest distance to " O   ALA A  51 " =    1.342
peak=   -3.516 closest distance to " O   PRO A 198 " =    1.296
peak=   -3.511 closest distance to " O   HOH Z 292 " =    4.390
peak=   -3.509 closest distance to " O   HOH Z 389 " =    1.755
peak=   -3.497 closest distance to " CG1 VAL A 112 " =    2.699
peak=   -3.480 closest distance to " NH2 ARG A  79 " =    1.899
peak=   -3.479 closest distance to " C   ASP A 231 " =    2.590
peak=   -3.478 closest distance to " O   HOH Z 389 " =    4.652
peak=   -3.462 closest distance to " CD1 LEU A 228 " =    2.147
peak=   -3.458 closest distance to " OG  SER A  26 " =    1.074
peak=   -3.445 closest distance to " O   HOH Z 196 " =    2.156
peak=   -3.441 closest distance to " CG  TRP A 266 " =    1.613
peak=   -3.440 closest distance to " O   HOH Z  52 " =    1.484
peak=   -3.439 closest distance to " NZ  LYS A 119 " =    3.431
peak=   -3.436 closest distance to " O   HOH Z  11 " =    1.836
peak=   -3.418 closest distance to " CB  ALA A  51 " =    1.816
peak=   -3.415 closest distance to " ND2 ASN A 187 " =    1.657
peak=   -3.412 closest distance to " O   ALA A 256 " =    1.544
peak=   -3.407 closest distance to " O   HOH Z 118 " =    2.798
peak=   -3.406 closest distance to " O   ASP A 231 " =    2.438
peak=   -3.399 closest distance to " N   THR A 235 " =    1.344
peak=   -3.399 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.399 closest distance to " CD1 ILE A 263 " =    2.705
peak=   -3.380 closest distance to " O   HOH Z 339 " =    1.827
peak=   -3.375 closest distance to " CD  LYS A 289 " =    2.521
peak=   -3.375 closest distance to " O   HOH Z 353 " =    2.204
peak=   -3.373 closest distance to " O   VAL A 197 " =    1.295
peak=   -3.370 closest distance to " O   HOH Z  15 " =    1.572
peak=   -3.364 closest distance to " O   HOH Z 311 " =    3.579
peak=   -3.359 closest distance to " CG  MET A 105 " =    0.915
peak=   -3.358 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.358 closest distance to " O   HOH Z 431 " =    1.690
peak=   -3.352 closest distance to " OD1 ASN A 249 " =    1.264
peak=   -3.351 closest distance to " CD1 PHE A  59 " =    1.867
peak=   -3.350 closest distance to " O   HOH Z 185 " =    2.244
peak=   -3.348 closest distance to " O   HOH Z 350 " =    1.844
peak=   -3.342 closest distance to " NH2 ARG A  66 " =    1.765
peak=   -3.341 closest distance to " CB  PRO A 163 " =    2.624
peak=   -3.332 closest distance to " O   HOH Z 234 " =    4.206
peak=   -3.331 closest distance to " CH2 TRP A 179 " =    1.376
peak=   -3.330 closest distance to " CA  GLY A 133 " =    2.186
peak=   -3.328 closest distance to " OD1 ASP A 200 " =    1.331
peak=   -3.323 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.323 closest distance to " OG1 THR A  82 " =    1.446
peak=   -3.312 closest distance to " CD  GLN A  88 " =    0.965
peak=   -3.311 closest distance to " O   HOH Z 385 " =    1.936
peak=   -3.309 closest distance to " C   GLN A  58 " =    2.293
peak=   -3.306 closest distance to " O   TRP A  70 " =    1.553
peak=   -3.304 closest distance to " O   HOH Z 292 " =    2.786
peak=   -3.303 closest distance to " O   HOH Z  19 " =    2.240
peak=   -3.303 closest distance to " O   HOH Z 388 " =    2.002
peak=   -3.302 closest distance to " O   HOH Z 222 " =    1.580
peak=   -3.300 closest distance to " O   PHE A 218 " =    1.600
peak=   -3.299 closest distance to " CE3 TRP A 150 " =    1.978
peak=   -3.297 closest distance to " OG  SER A   3 " =    1.620
peak=   -3.296 closest distance to " O   ASN A 187 " =    1.475
peak=   -3.293 closest distance to " ND2 ASN A  39 " =    1.382
peak=   -3.289 closest distance to " CB  ALA A  43 " =    2.287
peak=   -3.289 closest distance to " OG  SER A  87 " =    1.317
peak=   -3.282 closest distance to " C   ASN A 285 " =    2.357
peak=   -3.275 closest distance to " O   HOH Z 297 " =    2.716
peak=   -3.270 closest distance to " O   GLY A 196 " =    1.053
peak=   -3.269 closest distance to " OH  TYR A 172 " =    1.745
peak=   -3.268 closest distance to " O   HOH Z 191 " =    5.232
peak=   -3.258 closest distance to " O   HOH Z  19 " =    2.115
peak=   -3.253 closest distance to " CB  PHE A 192 " =    1.786
peak=   -3.251 closest distance to " O   HOH Z 211 " =    1.544
peak=   -3.246 closest distance to " O   HOH Z 193 " =    1.727
peak=   -3.244 closest distance to " OG  SER A 206 " =    1.603
peak=   -3.242 closest distance to " N   GLN A 122 " =    1.455
peak=   -3.234 closest distance to " OD1 ASP A 191 " =    1.614
peak=   -3.233 closest distance to " OH  TYR A 214 " =    1.299
peak=   -3.229 closest distance to " CG2 ILE A  20 " =    2.761
peak=   -3.228 closest distance to " CB  ASP A 132 " =    2.208
peak=   -3.228 closest distance to " O   HOH Z 148 " =    1.807
peak=   -3.227 closest distance to " O   HOH Z  47 " =    1.448
peak=   -3.225 closest distance to " CD  GLN A  58 " =    1.303
peak=   -3.223 closest distance to " CA  GLY A 203 " =    2.248
peak=   -3.220 closest distance to " O   HOH Z 359 " =    2.951
peak=   -3.213 closest distance to " CD1 TYR A 247 " =    2.453
peak=   -3.210 closest distance to " CE BMET A  47 " =    1.502
peak=   -3.208 closest distance to " CB  ALA A 227 " =    2.333
peak=   -3.205 closest distance to " O   SER A 210 " =    1.809
peak=   -3.202 closest distance to " CE  LYS A  76 " =    2.890
peak=   -3.202 closest distance to " O   HOH Z 427 " =    1.517
peak=   -3.198 closest distance to " C   MET A 188 " =    1.523
peak=   -3.196 closest distance to " C   LEU A 143 " =    1.069
peak=   -3.194 closest distance to " O   HOH Z 385 " =    2.215
peak=   -3.190 closest distance to " O   VAL A 174 " =    1.897
peak=   -3.188 closest distance to " OD1 ASN A 148 " =    1.534
peak=   -3.186 closest distance to " O   HOH Z 174 " =    2.317
peak=   -3.182 closest distance to " O   SER A  95 " =    1.507
peak=   -3.176 closest distance to " O   HOH Z 147 " =    1.969
peak=   -3.175 closest distance to " SG ACYS A 201 " =    1.892
peak=   -3.173 closest distance to " O   HOH Z 295 " =    1.393
peak=   -3.172 closest distance to " CG  GLU A 152 " =    2.348
peak=   -3.172 closest distance to " O   HOH Z  71 " =    1.233
peak=   -3.168 closest distance to " O   VAL A 125 " =    2.222
peak=   -3.168 closest distance to " CB  ALA A 114 " =    2.424
peak=   -3.155 closest distance to " O   HOH Z  90 " =    2.712
peak=   -3.154 closest distance to " CG  ASN A  45 " =    1.794
peak=   -3.153 closest distance to " CA  ASN A 127 " =    1.038
peak=   -3.152 closest distance to " CG  ARG A 219 " =    2.807
peak=   -3.142 closest distance to " SD BMET A  47 " =    2.810
peak=   -3.142 closest distance to " CD2 TYR A 293 " =    2.120
peak=   -3.142 closest distance to " O   HOH Z 310 " =    1.673
peak=   -3.141 closest distance to " CD  ARG A 195 " =    5.107
peak=   -3.141 closest distance to " N   GLN A  77 " =    1.600
peak=   -3.137 closest distance to " OD1 ASP A 191 " =    1.482
peak=   -3.135 closest distance to " O   HOH Z 344 " =    2.527
peak=   -3.133 closest distance to " O   HOH Z 278 " =    1.414
peak=   -3.132 closest distance to " OG BSER A 210 " =    2.041
peak=   -3.129 closest distance to " CG1 VAL A 125 " =    2.156
peak=   -3.129 closest distance to " O   GLY A 211 " =    1.343
peak=   -3.116 closest distance to " O   SER A  22 " =    2.173
peak=   -3.116 closest distance to " CG1 VAL A 197 " =    2.242
peak=   -3.113 closest distance to " O   HOH Z 283 " =    1.632
peak=   -3.105 closest distance to " O   HOH Z 281 " =    2.833
peak=   -3.104 closest distance to " O   HOH Z 148 " =    3.093
peak=   -3.095 closest distance to " O   HOH Z 410 " =    2.057
peak=   -3.085 closest distance to " N   MET A 105 " =    2.626
peak=   -3.071 closest distance to " CB  TRP A 266 " =    1.984
peak=   -3.063 closest distance to " O   TRP A  92 " =    1.721
peak=   -3.048 closest distance to " CG  PRO A 163 " =    2.712
peak=   -3.044 closest distance to " ND2 ASN A 252 " =    1.729
peak=   -3.039 closest distance to " N   ASP A 171 " =    2.440
peak=   -3.039 closest distance to " O   HOH Z 175 " =    4.299
peak=   -3.025 closest distance to " CE1 HIS A  81 " =    1.469
peak=   -3.010 closest distance to " O   ALA A 161 " =    1.212

================= 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    :  0.4496 0.4530   6.247475e+00   6.239829e+00
   1_bss:  0.4412 0.4416   6.243547e+00   6.224940e+00
   1_xyz:  0.3506 0.3741   6.092713e+00   6.131017e+00
   1_adp:  0.2946 0.3397   5.968121e+00   6.068314e+00
   1_occ:  0.2943 0.3402   5.967789e+00   6.069413e+00
   2_bss:  0.2898 0.3355   5.966022e+00   6.065141e+00
   2_xyz:  0.2118 0.2619   5.691921e+00   5.855221e+00
   2_adp:  0.1928 0.2406   5.610234e+00   5.785667e+00
   2_occ:  0.1925 0.2405   5.609575e+00   5.785590e+00
   3_bss:  0.1908 0.2394   5.607108e+00   5.782572e+00
   3_xyz:  0.1429 0.1876   5.342591e+00   5.554768e+00
   3_adp:  0.1315 0.1778   5.277780e+00   5.501999e+00
   3_occ:  0.1314 0.1777   5.277367e+00   5.501578e+00
   4_bss:  0.1317 0.1766   5.275510e+00   5.498232e+00
   4_xyz:  0.1200 0.1641   5.199893e+00   5.427799e+00
   4_adp:  0.1176 0.1621   5.185498e+00   5.415278e+00
   4_occ:  0.1175 0.1620   5.184921e+00   5.414687e+00
   5_bss:  0.1175 0.1619   5.184847e+00   5.414657e+00
   5_xyz:  0.1093 0.1582   5.137864e+00   5.389725e+00
   5_adp:  0.1091 0.1584   5.138636e+00   5.391596e+00
   5_occ:  0.1087 0.1583   5.136618e+00   5.390331e+00
   5_bss:  0.1087 0.1583   5.136426e+00   5.390158e+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:  0.353   9.310   7.088   7.912   9.756   0.000   0.000   0.000
   1_xyz:  0.353   9.310   7.088   7.912   9.756   0.000   0.000   0.000
   1_adp:  0.353   9.310   7.088   7.912   9.756   0.000   0.000   0.000
   1_occ:  0.353   9.310   7.088   7.912   9.756   0.000   0.000   0.000
   2_bss:  0.320  20.001   3.600   4.123   6.564   0.000   0.000   0.000
   2_xyz:  0.320  20.001   3.600   4.123   6.564   0.000   0.000   0.000
   2_adp:  0.320  20.001   3.600   4.123   6.564   0.000   0.000   0.000
   2_occ:  0.320  20.001   3.600   4.123   6.564   0.000   0.000   0.000
   3_bss:  0.324  33.320   2.416   2.926   4.162   0.000   0.000   0.000
   3_xyz:  0.324  33.320   2.416   2.926   4.162   0.000   0.000   0.000
   3_adp:  0.324  33.320   2.416   2.926   4.162   0.000   0.000   0.000
   3_occ:  0.324  33.320   2.416   2.926   4.162   0.000   0.000   0.000
   4_bss:  0.315  33.321   2.370   2.783   3.455   0.000   0.000   0.000
   4_xyz:  0.315  33.321   2.370   2.783   3.455   0.000   0.000   0.000
   4_adp:  0.315  33.321   2.370   2.783   3.455   0.000   0.000   0.000
   4_occ:  0.315  33.321   2.370   2.783   3.455   0.000   0.000   0.000
   5_bss:  0.317  35.202   2.370   2.783   3.455   0.000   0.000   0.000
   5_xyz:  0.317  35.202   2.370   2.783   3.455   0.000   0.000   0.000
   5_adp:  0.317  35.202   2.370   2.783   3.455   0.000   0.000   0.000
   5_occ:  0.317  35.202   2.370   2.783   3.455   0.000   0.000   0.000
   5_bss:  0.320  39.923  -0.460  -0.027   0.488   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.237 0.4934  0.5732    60753.453
   1_bss:  52.341 0.4892  0.7181    57380.817
   1_xyz:  41.912 0.6183  0.8950    39764.226
   1_adp:  36.809 0.6799  0.9873    32424.229
   1_occ:  36.876 0.6791  0.9862    32512.452
   2_bss:  36.528 0.6829  0.8752    31995.792
   2_xyz:  26.761 0.7920  0.9856    18019.899
   2_adp:  23.867 0.8233  1.0134    15192.400
   2_occ:  23.859 0.8234  1.0129    15173.873
   3_bss:  23.692 0.8250  0.9576    15048.341
   3_xyz:  17.713 0.8829  0.9895     8954.189
   3_adp:  16.480 0.8943  0.9920     8088.309
   3_occ:  16.468 0.8944  0.9919     8079.580
   4_bss:  16.400 0.8949  0.9811     8000.397
   4_xyz:  14.908 0.9075  0.9876     6878.867
   4_adp:  14.595 0.9103  0.9875     6708.339
   4_occ:  14.578 0.9105  0.9875     6699.962
   5_bss:  14.575 0.9105  0.9876     6702.047
   5_xyz:  14.112 0.9141  0.9884     6367.834
   5_adp:  14.138 0.9140  0.9844     6392.748
   5_occ:  14.112 0.9142  0.9842     6377.815
   5_bss:  14.108 0.9142  0.9855     6378.822
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3251e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3251e+01
   1_xyz:   1.583  0.012  0.104 18.033  0.006  4.109   1.2589e-01
   1_adp:   1.583  0.012  0.104 18.033  0.006  4.109   1.2589e-01
   1_occ:   1.583  0.012  0.104 18.033  0.006  4.109   1.2589e-01
   2_bss:   1.583  0.012  0.104 18.033  0.006  4.109   1.2589e-01
   2_xyz:   0.985  0.006  0.071 15.820  0.004  4.121   6.1741e-02
   2_adp:   0.985  0.006  0.071 15.820  0.004  4.121   6.1741e-02
   2_occ:   0.985  0.006  0.071 15.820  0.004  4.121   6.1741e-02
   3_bss:   0.985  0.006  0.071 15.820  0.004  4.121   6.1741e-02
   3_xyz:   1.002  0.006  0.075 15.663  0.004  4.109   6.0007e-02
   3_adp:   1.002  0.006  0.075 15.663  0.004  4.109   6.0007e-02
   3_occ:   1.002  0.006  0.075 15.663  0.004  4.109   6.0007e-02
   4_bss:   1.002  0.006  0.075 15.663  0.004  4.109   6.0007e-02
   4_xyz:   0.934  0.005  0.072 15.617  0.003  4.110   5.5243e-02
   4_adp:   0.934  0.005  0.072 15.617  0.003  4.110   5.5243e-02
   4_occ:   0.934  0.005  0.072 15.617  0.003  4.110   5.5243e-02
   5_bss:   0.934  0.005  0.072 15.617  0.003  4.110   5.5243e-02
   5_xyz:   1.103  0.008  0.087 15.783  0.004  4.109   7.0715e-02
   5_adp:   1.103  0.008  0.087 15.783  0.004  4.109   7.0715e-02
   5_occ:   1.103  0.008  0.087 15.783  0.004  4.109   7.0715e-02
   5_bss:   1.103  0.008  0.087 15.783  0.004  4.109   7.0715e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9026e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9026e+00
   1_xyz:  13.493  0.150  0.454 86.694  0.051  2.237   9.0245e-02
   1_adp:  13.493  0.150  0.454 86.694  0.051  2.237   9.0245e-02
   1_occ:  13.493  0.150  0.454 86.694  0.051  2.237   9.0245e-02
   2_bss:  13.493  0.150  0.454 86.694  0.051  2.237   9.0245e-02
   2_xyz:   6.374  0.065  0.265 86.015  0.036  2.307   4.3371e-02
   2_adp:   6.374  0.065  0.265 86.015  0.036  2.307   4.3371e-02
   2_occ:   6.374  0.065  0.265 86.015  0.036  2.307   4.3371e-02
   3_bss:   6.374  0.065  0.265 86.015  0.036  2.307   4.3371e-02
   3_xyz:   6.829  0.044  0.429 86.502  0.030  2.366   4.8548e-02
   3_adp:   6.829  0.044  0.429 86.502  0.030  2.366   4.8548e-02
   3_occ:   6.829  0.044  0.429 86.502  0.030  2.366   4.8548e-02
   4_bss:   6.829  0.044  0.429 86.502  0.030  2.366   4.8548e-02
   4_xyz:   7.005  0.034  0.420 82.103  0.031  2.375   3.7089e-02
   4_adp:   7.005  0.034  0.420 82.103  0.031  2.375   3.7089e-02
   4_occ:   7.005  0.034  0.420 82.103  0.031  2.375   3.7089e-02
   5_bss:   7.005  0.034  0.420 82.103  0.031  2.375   3.7089e-02
   5_xyz:   6.926  0.045  0.629 82.624  0.037  2.259   5.6415e-02
   5_adp:   6.926  0.045  0.629 82.624  0.037  2.259   5.6415e-02
   5_occ:   6.926  0.045  0.629 82.624  0.037  2.259   5.6415e-02
   5_bss:   6.926  0.045  0.629 82.624  0.037  2.259   5.6415e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  57.10   0.00  11.31  57.10   0.00   8.61  56.55   0.00  26.02
   1_occ:  57.10   0.00  11.31  57.10   0.00   8.61  56.55   0.00  26.02
   2_bss:  57.10   0.00  11.31  57.10   0.00   8.61  56.55   0.00  26.02
   2_xyz:  57.10   0.00  11.31  57.10   0.00   8.61  56.55   0.00  26.02
   2_adp:  64.40   0.00  11.71  64.40   0.00   8.16  61.78   1.49  31.02
   2_occ:  64.40   0.00  11.71  64.40   0.00   8.16  61.78   1.49  31.02
   3_bss:  64.40   0.00  11.71  64.40   0.00   8.16  61.78   1.49  31.02
   3_xyz:  64.40   0.00  11.71  64.40   0.00   8.16  61.78   1.49  31.02
   3_adp:  76.50   0.00  12.44  76.50   0.00   8.12  72.32   2.38  35.92
   3_occ:  76.50   0.00  12.44  76.50   0.00   8.12  72.32   2.38  35.92
   4_bss:  76.50   0.00  12.44  76.50   0.00   8.12  72.32   2.38  35.92
   4_xyz:  76.50   0.00  12.44  76.50   0.00   8.12  72.32   2.38  35.92
   4_adp:  83.86   0.00  12.44  83.86   0.00   8.11  77.19   1.66  36.04
   4_occ:  83.86   0.00  12.44  83.86   0.00   8.11  77.19   1.66  36.04
   5_bss:  83.86   0.00  12.44  83.86   0.00   8.11  77.19   1.66  36.04
   5_xyz:  83.86   0.00  12.44  83.86   0.00   8.11  77.19   1.66  36.04
   5_adp:  84.76   0.00  12.33  84.76   0.00   8.02  77.39   1.11  35.82
   5_occ:  84.76   0.00  12.33  84.76   0.00   8.02  77.39   1.11  35.82
   5_bss:  87.67   2.91  15.24  87.67   2.91  10.93  80.30   4.01  38.73
------------------------------------------------------------------------
 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:    1.202    0.020    0.404
   1_adp:    1.202    0.020    0.404
   1_occ:    1.202    0.020    0.404
   2_bss:    1.202    0.020    0.404
   2_xyz:    1.513    0.030    0.529
   2_adp:    1.513    0.030    0.529
   2_occ:    1.513    0.030    0.529
   3_bss:    1.513    0.030    0.529
   3_xyz:    1.427    0.013    0.583
   3_adp:    1.427    0.013    0.583
   3_occ:    1.427    0.013    0.583
   4_bss:    1.427    0.013    0.583
   4_xyz:    1.569    0.030    0.606
   4_adp:    1.569    0.030    0.606
   4_occ:    1.569    0.030    0.606
   5_bss:    1.569    0.030    0.606
   5_xyz:    1.555    0.024    0.621
   5_adp:    1.555    0.024    0.621
   5_occ:    1.555    0.024    0.621
   5_bss:    1.555    0.024    0.621
------------------------------------------------------------------------

CPU time actual refinement: 334.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/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/trial/run_540/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_540/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.00 
  Macro-tasks:
    bulk solvent and scale       = 46.26  
    individual site refinement   = 136.02 
    weights calculation          = 31.45  
    collect and process          = 6.51   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.36 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 101.15 
    alpha_beta                      = 8.24   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 111.11 
    fmodel                         = 7.93   
    r_factors                      = 0.28   
    phase_errors                   = 10.80  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 242.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.701 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    643 calls, 100.79 s
gradients_fft:          587 calls,  98.06 s

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

# Date 2008-01-16 Time 01:50:39 PST -0800 (1200477039.03 s)
Start R-work = 0.4496, R-free = 0.4530 (no bulk solvent and anisotropic scale)
Final R-work = 0.1262, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.4412, R-free = 0.4416
Final R-work = 0.1087, R-free = 0.1583